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  • Essen : Verl. Glückauf
  • International Union of Crystallography (IUCr)
  • Krefeld : Geologischer Dienst Nordhein-Westfalen
  • 2015-2019
  • 2005-2009
  • 2000-2004  (2,467)
  • 1980-1984
  • 2001  (2,467)
Collection
Publisher
Years
  • 2015-2019
  • 2005-2009
  • 2000-2004  (2,467)
  • 1980-1984
Year
  • 1
    Electronic Resource
    Electronic Resource
    Structural study of monoclinic KGd(WO4)2 and effects of lanthanide substitution (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 1-6 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The crystal structure of monoclinic KGd(WO4)2 (KGW) has been refined at room temperature by using single-crystal X-ray diffraction data. The unit-cell parameters are a = 10.652 (4), b = 10.374 (6), c = 7.582 (2) Å, β = 130.80 (2)°, with Z = 4, in space group C2/c. The linear thermal expansion tensor has been determined and the principal axes are [302], [010] and [106]. The principal axis with maximum thermal expansion (\boldalpha'_{33} = 23.44 × 10−6 K−1), {\bf X}'_{3}, was located 12° from the c axis. Undoped crystals of KGW and crystals that were partially doped by Pr, Nd, Ho, Er, Tm and Yb were grown by the top-seeding-solution growth slow-cooling method. The effect of doping on the KGW structure was observed in the cell parameters and in morphological changes. The changes in parameters follow the changes in lanthanide ionic radii. The doped crystals show {021} and {\bar{2}21} faces in addition to the {110}, {\bar{1}11}, {010}, {130} and {310} faces which basically follow the habit of the undoped KGW crystals. The development of the faces is related to the number of the most important periodic bond chains parallel to them.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889800013352
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  • 2
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    Small-angle X-ray scattering by PVP–water mixtures (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 62-64 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Small-angle X-ray scattering experiments reveal the formation of large-scale structures when a 60 wt% poly(vinylpyrrolidone) (PVP)–water mixture is cooled to 260 K. The formation of these structures leads to an enhancement of continuous small-angle scattering with decreasing temperature. This is accompanied by the appearance of sharp Bragg peaks that have a very short lifetime. The scattering angles of these peaks are in accordance with a hexagonal columnar structure. It appears that such structures occasionally live long enough to undergo rotational Brownian motion.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889800018689
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  • 3
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    Aminoguanidinium hexafluorozirconate: a new ferroelectric (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 47-54 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Analysis of the atomic arrangement in anhydrous aminoguanidinium hexafluorozirconate, CN4H8ZrF6, reported by Bukvetskii, Gerasimenko & Davidovich [Koord. Khim. (1990), 16, 1479–1484], led to the prediction that it is a new ferroelectric [Abrahams, Mirsky & Nielson (1996). Acta Cryst. B52, 806–809]. Initial attempts to verify the prediction were inconclusive because of the variety of closely related materials produced under the original preparation conditions. Clarification of these conditions led to the formation of pure CN4H8ZrF6 and the growth of single crystals with dimensions as large as 7 × 7 × 2 mm. Highly reproducible calorimetric and dielectric permittivity anomalies reveal the Curie temperature Tc = 383 (1) K. At this temperature, the heat capacity Cp exhibits an entropy change of 0.7 (1) J mol−1 K−1, while the relative permittivity εr exhibits an inflection and the dielectric loss a distinct peak; the dielectric anomaly at Tc is observed only at the lowest (0.1–1 kHz) frequencies used. Dielectric hysteresis is demonstrable at 295 K under the application of ∼1 MV m−1 alternating fields and remains observable at all T 〈 Tc but not at T ≥ Tc; the prediction of ferroelectricity is hence confirmed. The value of the spontaneous polarization Ps is 0.45 (9) × 10−2 C m−2 at 298 K, with piezoelectric coefficient d33 = 1.9 (5) pC N−1 and pyroelectric coefficient p3 = 4 (1) µC m−2 K−1. Tilts of less than ∼11° by the two symmetry-independent CN4H{}_{8}^{2+} ions, combined with rotations of ∼20° or less by the N—NH3 and C—(NH2)2 groups about the central C—N bond in each cation, as all H atoms rotate into or become symmetrically distributed about the planes at z = 0 or ½, allow them to conform to mirror symmetry via polar atomic displacements of ∼0.4 Å or less by N or C, and of 0.7 Å or less by H. Corresponding displacements of less than 0.08 Å within the two symmetry-independent ZrF{}_{6}^{2-} anions also result in mirror symmetry, satisfying the structural criteria required for the development of ferroelectricity.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889800015508
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  • 4
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    André Guinier (1911–2000) (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 88-88 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889800011432
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  • 5
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    Harry Brumberger (1926–2000) (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 88-88 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889801000966
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  • 6
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    A very simple and cheap greasing device for crystallization plates (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 224-224 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A device to grease a 24-well crystallization plate can be easily made with a disposable plastic syringe and a sample-retention vial from a centrifugal filter device. It takes only 2 min to grease one plate with the device.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889800018951
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  • 7
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    Global indicators of X-ray data quality (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 130-135 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Global indicators of the quality of diffraction data are presented and discussed, and are evaluated in terms of their performance with respect to various tasks. Based on the results obtained, it is suggested that some of the conventional indicators still in use in the crystallographic community should be abandoned, such as the nominal resolution dmin or the merging R factor Rmerge, and replaced by more objective and more meaningful numbers, such as the effective optical resolution deff,opt and the redundancy-independent merging R factor Rr.i.m.. Furthermore, it is recommended that the precision-indicating merging R factor Rp.i.m. should be reported with every diffraction data set published, because it describes the precision of the averaged measurements, which are the quantities normally used in crystallography as observables.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889800018227
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  • 8
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    An X-ray interferometer with a large and variable path length difference (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 166-171 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The first chromatic hard X-ray interferometer with a large and variable path length difference has been built and successfully tested. Interference fringe visibility was measured as a function of the path length difference. Based on the measurements, fringe visibility analysis was performed to give the transmitted beam coherence lengths. The results agree very well with expected coherence values based on the angular and spectral acceptances of the interferometer.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889801002072
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  • 9
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    The reliability index R2 as a versatile tool in structure analysis of inorganic and small molecular compounds (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 178-186 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Applications of R_2 in small-molecule crystallography are described. Ways of using R_2 to evaluate initial models of a structure are discussed. These models, obtained from Patterson methods, are usually small. They may include one or more heavy atoms and pseudosymmetry is sometimes present in the model. The R_2 criterion is used also to identify misplaced atoms prior to the start of the expansion process. Finally, R_2 is used during structure expansion by the application of phase refinement or Fourier methods. Details of the procedures of extension, as well as the role of R_2 therein, are presented and evaluated. Results obtained with various test structures are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889801000668
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  • 10
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    EXPGUI, a graphical user interface for GSAS (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 210-213 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A description and justification of the EXPGUI program is presented. This program implements a graphical user interface and shell for the GSAS single-crystal and Rietveld package. Use of the Tcl/Tk scripting language allows EXPGUI to be platform independent. Also included is a synopsis of how the program is implemented.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889801002242
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  • 11
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    Harry Brumberger (1926–2000) (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 225-225 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
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    URL: http://dx.doi.org/10.1107/S0021889801004642
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  • 12
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    Neutron transmission through pyrolytic graphite monochromators (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 258-262 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Thermal neutron transmission measurements have been made as a function of wavelength on a pyrolytic graphite monochromator crystal that has been set to diffract a horizontal beam at different take-off angles. The major dips in the transmission caused by the various reflections have been identified. These results can be used for the design of a beamline on which more than one instrument is placed. The transmission data show that it is best for the monochromator with the greatest (horizontal) take-off angle to be placed upstream, with monochromators with decreasing take-off angles progressively further downstream. The order of instruments for which the wavelength is greater than 0.43 nm is unimportant.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889801002254
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  • 13
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    Orientation distribution analysis in deformed grains (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 280-288 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Some improvements are proposed for the statistical analysis of orientation data within individual grains, in particular by allowing for crystallographic symmetries. A method based on quaternions is then presented to characterize orientation spreads including anisotropic effects. Based on this approach, some analyses of disorientation distributions (orientation distribution functions, disorientation noise and the description of sub-boundary disorientation) are reconsidered. The analysis is illustrated by a practical application to the microtextures of a hot deformed aluminium alloy crystal.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889801003077
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  • 14
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    Microstructural transformation of vanadium pentoxide powder obtained by high-energy vibrational ball-milling (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 381-385 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: An X-ray powder profile analysis of vanadium pentoxide powder milled in a high-energy vibrational ball-mill is presented. The strain- and size-induced broadening of the Bragg reflection for two different crystallographic directions ([001] and [100]) were determined by Warren–Averbach (WA) analysis, using a pattern-decomposition method assuming a pseudo-Voigt function. The deformation process causes a decrease in the domain size, and a near isotropic saturation value of ∼10 nm is reached after severe milling. The initial stages of milling produce a propensity for size broadening, whereas, with increasing milling time, microstrain broadening is predominant. WA analysis indicated significant plastic strain along with spatial confinement of the internal strain fields, probably in the crystallite interfaces. Transmission electron microscopy revealed a drastic change in particle shape after 64 h of milling, indicating the existence of size anisotropy which, however, decreased with further increase of the milling time.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889801004009
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  • 15
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    New approach to stress analysis based on grazing-incidence X-ray diffraction (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 427-435 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A new development in the determination of residual stresses in thin surface layers and coatings is presented. The procedure, based on the grazing-incidence X-ray diffraction geometry (referred to here as the `g-sin2 ψ' geometry), enables non-destructive measurement at a chosen depth below the sample surface. The penetration depth of the X-ray radiation is well defined and does not change during the experiment. The method is particularly useful for the analysis of non-uniform stresses in near-surface layers. The g-sin2 ψ geometry was applied for measurements of the residual stresses in TiN coatings. Anisotropic diffraction elastic constants of textured material were used to determine the stress value from the measured lattice strains. A new method of data treatment enables reference-free measurements of residual stresses.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889801005404
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  • 16
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    Neutron Laue diffraction experiments on a large unit cell: concanavalin A complexed with methyl-α-D-glucopyranoside (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 454-457 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A neutron Laue diffraction experiment on a complex of concanavalin A with methyl-α-D-glucopyranoside extensively soaked in D2O (space group I213, a = 167.8 Å), which resulted in 3.5 Å diffraction data, is described. In a programme of structural studies of crystalline saccharide complexes of concanavalin A, the unit cell of the cubic I213 complex of concanavalin A with methyl-α-D-glucopyranoside is one of the largest. With its cell edge of 167.8 Å and its asymmetric unit of molecular weight 50 kDa, it represents a challenge for current neutron diffraction technology. The size of the crystal used in this experiment, although large (4 × 3 × 2 mm), was not the largest ever produced for this complex. The degree of spatial overlapping observed in the Laue experiment, however, suggests that use of larger crystals would be a disadvantage. On the basis of these observations, several technical improvements for macromolecular neutron crystallography are suggested.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889801007245
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  • 17
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    European Crystallography Prize (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 537-537 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
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    URL: http://dx.doi.org/10.1107/S0021889801011487
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  • 18
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    Structural and morphological investigation of amorphous hydrogenated silicon carbide (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 465-472 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Amorphous hydrogenated silicon carbide thin films were deposited by plasma enhanced chemical vapor deposition (PECVD) at temperatures ranging from 573 to 623 K, with different concentrations of silane and methane, exploring two deposition parameters: the radio frequency (r.f.) power and the hydrogen dilution. The aim of the work was to induce, predominantly, the formation of Si—C heteronuclear bonds in a homogeneous network. The composition was determined by Rutherford backscattering and the chemical bonding by Fourier transform infrared spectrometry. The local structural order was analyzed by means of extended X-ray absorption fine structure at the Si K edge. The morphology was investigated by small-angle X-ray scattering in order to determine the possible presence of voids in the amorphous matrix. The morphological investigation was completed by transmission electron microscopy. Better-structured films were obtained for a composition close to stoichiometry, grown with an r.f. power of 100 W and with 300 s.c.c.m. (standard cubic centimeter per minute) of hydrogen dilution.
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    URL: http://dx.doi.org/10.1107/S0021889801007889
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  • 19
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    Correction for thermal diffuse scattering in single-crystal time-of-flight neutron diffraction: first applications (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 493-495 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The thermal diffuse scattering (TDS) correction developed by Popa & Willis [Acta Cryst. (1997), A53, 537–545] for single-crystal pulsed neutron diffraction is examined via a series of experimental data sets collected at the spallation neutron source IPNS. The effect on the derived temperature parameter values is assessed and compared with reference structures obtained from gamma-ray diffraction. The importance of carrying out TDS corrections is emphasized. Suggestions are made regarding the method of evaluation of the TDS in situations where the elastic constants are unknown.
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    URL: http://dx.doi.org/10.1107/S0021889801009426
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  • 20
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    SIR2000-N, a program for large and small crystal structures (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 523-526 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The program SIR2000 [Burla et al. (2000). Acta Cryst. A56, 451–457] was designed for the ab initio solution of macromolecular crystal structures, provided that the data resolution is no lower than 1.2 Å. As the phasing procedure of SIR2000 is rather time consuming, modifications have been introduced to improve its efficiency and to make it additionally suitable for small molecules (new version SIR2000-N). The role of the tangent refinement in modern phasing procedures is enlightened.
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    URL: http://dx.doi.org/10.1107/S0021889801005672
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  • 21
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    Modelling of small-angle X-ray scattering data using Hermite polynomials (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 510-518 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A new algorithm, called the term-selection algorithm (TSA), is derived to treat small-angle X-ray scattering (SAXS) data by fitting models to the scattering intensity using weighted Hermite polynomials. This algorithm exploits the orthogonal property of the Hermite polynomials and introduces an error-reduction ratio test to select the correct model terms or to determine which polynomials are to be included in the model and to estimate the associated unknown coefficients. With no a priori information about particle sizes, it is possible to evaluate the real-space distribution function as well as three- and one-dimensional correlation functions directly from the models fitted to raw experimental data. The success of this algorithm depends on the choice of a scale factor and the accuracy of orthogonality of the Hermite polynomials over a finite range of SAXS data. An algorithm to select a weighted orthogonal term is therefore derived to overcome the disadvantages of the TSA. This algorithm combines the properties and advantages of both weighted and orthogonal least-squares algorithms and is numerically more robust for the estimation of the parameters of the Hermite polynomial models. The weighting feature of the algorithm provides an additional degree of freedom to control the effects of noise and the orthogonal feature enables the reorthogonalization of the Hermite polynomials with respect to the weighting matrix. This considerably reduces the error in orthogonality of the Hermite polynomials. The performance of the algorithm has been demonstrated considering both simulated data and experimental data from SAXS measurements of dewaxed cotton fibre at different temperatures.
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    URL: http://dx.doi.org/10.1107/S0021889801006951
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  • 22
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    M. A. Viswamitra (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 537-537 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
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    URL: http://dx.doi.org/10.1107/S002188980100886X
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  • 23
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    Contribution to X-ray analysis of carbo-nitrided steel layers (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 549-557 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The non-destructive X-ray diffraction method is used to analyse carbo-nitrided steel layers after wear testing. These measurements are carried out on the two major phases of the material, i.e. the martensite and the retained austenite. Such measurements are particularly difficult for three reasons. First, strong gradients exist across the wear track. Second, the diffraction peaks obtained for the martensite are broadened, as a result of the overlap of different reflections of the tetragonal structure. Third, the studied material is multiphase. Its major phases are martensite and austenite, but it also contains carbide and nitride clusters, which lead to incoherent scattering of X-rays. A new quantitative phase analysis method is thus proposed to define the volume fractions of these different constituents of the material. This method accounts for the evolution of the background level during wear. A micro-mechanical model is then developed to process the diffraction peak positions obtained for the martensite and the retained austenite. This model defines the `true' stress and carbon content of both phases. It also allows separation of the reflections of the martensite. The true widths of the diffraction peaks, which characterize the plastic deformation, can thus be quantified. Results for wear-test specimens show a strong plastic deformation of the retained austenite during contact fatigue. This leads to a partial transformation of this phase into martensite. In the martensite, on the contrary, the plastic deformation remains low but the carbon content decreases. This is caused by a stress-induced precipitation of carbides.
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    URL: http://dx.doi.org/10.1107/S0021889801008810
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  • 24
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    On the diffractive determination of single-crystal elastic constants using polycrystalline samples (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 585-601 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The diffractive determination of single-crystal elastic constants using polycrystalline samples represents the inverse problem to the (`direct') experiment of conventional diffractive residual-stress analysis. Both problems are rather sensitive to the quality of the experimental data and to the applied micro-mechanical models. This especially holds for the case of samples for which texture cannot be neglected. The current methods in the field are briefly described and specific difficulties are discussed. The key relations for the BPGeo micro-mechanical model (in which a texture-weighted geometric mean is applied in the stress analysis) are given for the general case. The necessity for careful analysis of the reliability of the results of planned experiments using theoretically modelled `experimental' data obtained with the applied micro-mechanical models is demonstrated for a set of line-shift data from a uniaxial tensile experiment on steel. The possibility of resolving the so-called d0 problem using the original line-position data for a structure refinement is demonstrated.
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    URL: http://dx.doi.org/10.1107/S0021889801010482
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    Simulation of electron density maps for two-dimensional crystal structures using Mathematica (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 658-660 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The simulations presented here are based on the program Mathematica as a tool to present electron density maps of two-dimensional crystal structures. The models give further insights into the relationship between the thermal displacement parameters and the quality of the electron density maps. Furthermore, users can readily test the effects of several crystallographic parameters on the electron density maps, such as, the number of reflections, the thermal displacement parameters and the unit-cell dimensions.
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    Ultrafine nanostructure of partially crystallized bulk amorphous Zr54.5Ti7.5Al10Cu20Ni8 (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 666-668 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Bulk amorphous Zr54.5Ti7.5Al10Cu20Ni8 was investigated by means of small-angle neutron scattering and high-resolution electron microscopy. Partially crystallized states were generated by annealing. The scattering data were analyzed in terms of a model taking into account both properties of the particles and interparticle interference. The mean radius of the particles is 1.3 nm. They are surrounded by a depletion zone with mean thickness of 2.6 nm. The volume fraction of the particles is estimated from the interparticle interference effect; its upper limit after annealing at 653 K for 4 h is 12%. Electron microscopy confirms the size determined from the scattering data and shows that the particles are crystalline.
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    Measurement of subtle strain modifications in heterostructures by using X-ray mapping in reciprocal space (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 715-721 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The application of X-ray mapping in reciprocal space to the measurement of subtle strain modifications in heterostructures is analysed, focussing on strain analysis in non-cubic crystals. Special attention is paid to the enhancement of the precision of the mapping technique in comparison with conventional diffraction profile measurements. The capabilities of the mapping-based strain analysis are illustrated by selected examples of epitaxially grown structures (obeying Vegard's rule), as well as implanted structures with unknown mismatches between the lattice parameters of the damaged layer and of the crystal bulk.
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    URL: http://dx.doi.org/10.1107/S0021889801013759
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    A furnace for in situ X-ray diffraction studies of insertion processes in electrode materials at elevated temperatures (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 654-657 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A furnace is described for in situ X-ray diffraction studies, in transmission mode, of structural changes in electrode materials for Li-ion (polymer) batteries in the ambient to 300°C temperature range. The method exploits the thin flat-cell geometry of the lithium-polymer battery concept. The flat sample is able to oscillate about a horizontal axis in its own plane in the X-ray beam, to provide better averaging during the diffraction experiment. The use of the device is demonstrated in a study of lithium intercalation in graphite (a commonly used anode material in lithium-ion batteries) during electrochemical cycling and storage at 70°C.
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    URL: http://dx.doi.org/10.1107/S0021889801011864
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    MWP-fit: a program for multiple whole-profile fitting of diffraction peak profiles by abinitio theoretical functions (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 669-676 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A computer program has been developed for the determination of microstructural parameters from diffraction profiles of materials with cubic or hexagonal crystal lattices. The measured profiles or their Fourier transforms are fitted by ab initio theoretical functions for size and strain broadening. In the calculation of the theoretical functions, it is assumed that the crystallites have log-normal size distribution and that the strain is caused by dislocations. Strain and size anisotropy are taken into account by the dislocation contrast factors and the ellipticity of the crystallites. The fitting procedure provides the median and the variance of the size distribution and the ellipticity of the crystallites, and the density and arrangement of the dislocations. The efficiency of the program is illustrated by examples of severely deformed copper and ball-milled lead sulfide specimens.
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    Planar faults in layered Bi-containing perovskites studied by X-ray diffraction line profile analysis (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 699-703 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Profile fitting procedures associated with integral breadth studies and Fourier analysis are applied to the study of the complex Bi-containing layered perovskite SrBi2Nb2O9. Strong line broadening anisotropy is evidenced. Both `size' and `strain' effects contribute to the observed width. However, `size' broadening along the [00l] direction is essentially caused by stacking faults. The coherently diffracting domain sizes are deduced from Fourier analysis of the diffraction patterns and a rough estimate of the mean distance between faults is given. Thermal annealing significantly decreases the stacking fault density.
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    Recombinant chemosensory protein (CSP2) from the moth Mamestra brassicae: crystallization and preliminary crystallographic study (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 137-139 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Chemosensory proteins (CSPs) are small proteins (13 kDa on average) present in several sensory organs from a wide range of insect species. They are believed to be involved in chemoperception (olfaction or taste) and to play a role in chemical transport from air or water to chemosensitive receptors. Here, the first crystals of a CSP originating from the moth Mamestra brassicae (Mbra) proboscis and expressed as recombinant protein in Escherichia coli periplasm are reported. Crystals of MbraCSP2 were obtained by the hanging-drop vapour-diffusion method under the following conditions: 1 µl of a 46 mg ml−1 protein solution in 50 mM Tris pH 8.0 containing cetyl alcohol as ligand (1:5 molar ratio) was mixed with 1 µl of well solution containing 30% PEG 4000, 0.2 M sodium acetate in 100 mM Tris at pH 8.4. The protein–cetyl alcohol complex crystallizes in space group P21, with unit-cell parameters a = 47.9, b = 49.7, c = 50.3 Å, β = 110.1°. With two molecules in the asymmetric unit, the VM is 2.15 Å3 Da−1 and the solvent content is 42%. A complete data set has been collected at 1.6 Å resolution on beamline ID14-2 (ESRF, Grenoble). Se-Met expression has been performed with a view to solving the CSP2 structure with MAD data collection using the Se absorption edge.
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    Structure of an RNA duplex with an unusual G·C pair in wobble-like conformation at 1.6 Å resolution (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 219-224 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of the RNA duplex r(CUGGGCGG)·r(CCGCCUGG) has been determined at 1.6 Å resolution and refined to a final R factor of 18.3% (Rfree = 24.1%). The sequence of the RNA fragment resembles domain E of Thermus flavus 5S rRNA. A previously undescribed wobble-like G·C base-pair formation is found. Owing to the observed hydrogen-bond network, it is proposed that the cytosine is protonated at position N3. The unusual base-pair formation is presumably strained by intermolecular interactions. In this context, crystal packing and particular intermolecular contacts may have direct influence on the three-dimensional structure. Furthermore, this structure includes two G·U wobble base pairs in tandem conformation, with the purines forming a so-called `cross-strand G stack'.
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    Practical experience with the use of halides for phasing macromolecular structures: a powerful tool for structural genomics (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 239-249 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of pepstatin-insensitive carboxyl proteinase (PCP) from Pseudomonas sp. 101, an enzyme with no overall sequence similarity to any other proteinases of known structure, was solved using crystals soaked in sodium bromide solution and then cryocooled. A data set collected at the bromine peak absorption wavelength was sufficient for calculation of an excellent map and the entire process of phasing and tracing the maps required almost no direct human intervention. The process of structure solution using single-wavelength data was compared with three-wavelength multiwavelength anomalous diffraction (MAD); although the latter resulted in slightly better maps, the use of this much more labor-intensive approach did not significantly improve the ability to solve the structure. The successful phasing approaches are compared with several less successful attempts utilizing other crystal forms of the enzyme and the practical aspects of the use of bromine as a heavy-atom derivative are discussed. In conclusion, the use of halides with single-wavelength diffraction data fulfills the requirements of being a first-choice method of high-throughput structure solution for the emerging field of structural genomics.
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    Crystallization and preliminary crystallographic studies of an antimicrobial protein from Pharbitis nil (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 263-265 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: An antimicrobial protein from seeds of Pharbitis nil (Pn-AMP) which shows an antifungal activity towards several agriculturally important plant pathogens has been crystallized in the presence of equimolar N-acetylglucosamine with sodium citrate as precipitant. The crystal belongs to the hexagonal space group P6122 (or P6522), with unit-cell parameters a = b = 29.33 (5), c = 133.44 (12) Å. Native data were collected using a crystal at 100 K to a resolution of 1.78 Å.
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    Structure of the M148Q mutant of rusticyanin at 1.5 Å: a model for the copper site of stellacyanin (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 355-360 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The small blue copper protein rusticyanin from Thiobacillus ferrooxidans contains a type 1 Cu centre with a single axial ligand, Met148, which together with the His-Cys-His trigonal planar ligands produces a distorted trigonal pyramidal coordination geometry to copper. Type 1 Cu sites are found in cupredoxins and several multicopper proteins, including oxidases and nitrite reductases. The role of the axial ligand has been extensively debated in terms of its function in the fine tuning of the redox potential and spectroscopic properties of type 1 Cu sites. Numerous mutations of the Met ligand in azurins have been studied, but interpretation of the results has been complicated by the presence of the additional carbonyl oxygen ligand from Gly45, a neighbouring residue to the coordinating His46. The importance of the axial ligand has been further emphasized by the finding that the type 1 centre in Rhus vernicifera stellacyanin, with the lowest redox potential in a type 1 Cu site of 184 mV, has Gln as the axial ligand, whilst fungal laccase and ceruloplasmin, which have redox potentials of 550–800 mV, have a Leu in this position. Here, the crystal structure of the M148Q mutant of rusticyanin at 1.5 Å resolution is presented. This is a significantly higher resolution than that of the structures of native rusticyanin. In addition, the M148Q structure is that of the oxidized protein while the native structures to date are of the reduced protein. The mutant protein crystallizes with two molecules per asymmetric unit, in contrast to the one present in the native crystal form. This mutant's redox potential (550 mV at pH 3.2) is lowered compared with that of the native protein (∼670 mV at pH 3.2) by about 120 mV. The type 1 Cu site of M148Q closely mimics the structural characteristics of the equivalent site in non-glycosylated cucumber stellacyanin (redox potential ∼260 mV) and, owing to the absence in rusticyanin of the fifth, carbonyl ligand present in azurin, may provide a better model for the R. vernicifera stellacyanin (redox potential ∼184 mV) type 1 Cu site, which also lacks the fifth ligand. Furthermore, the presence of two molecules in the asymmetric unit cell indicates a potential binding region of the redox partners.
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    Geometry of metal–ligand interactions in proteins (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 401-411 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The geometry of metal–ligand interactions in proteins is examined and compared with information for small-molecule complexes from the Cambridge Structural Database (CSD). The paper deals with the metals Ca, Mg, Mn, Fe, Cu, Zn and with metal–donor atom distances, coordination numbers and extent of distortion from ideal geometry (octahedral, tetrahedral etc.). It assesses the agreement between geometry found in all metalloprotein structures in the Protein Data Bank (PDB) determined at resolution ≤ 1.6 Å with that predicted from the CSD for ligands which are analogues of amino-acid side chains in proteins [Harding (1999), Acta Cryst. D55, 1432–1443; Harding (2000), Acta Cryst. D56, 857–867]. The agreement is reasonably good for these structures but poorer for many determined at lower resolution (examined to 2.8 Å resolution). For metal–donor distances, the predictions from the CSD, with minor adjustments, provide good targets either for validation or for restraints in refinement of structures where only poorer resolution data is available. These target distances are tabulated and the use of restraints is recommended. Validation of angles or the use in refinement of restraints on angles at the metal atom is more difficult because of the inherent flexibility of these angles. A much simplified set of parameters for angle restraints with quite large standard deviations is provided. (Despite the flexibility of the angles, acceptable and preferred coordination numbers and shapes are well established and a summary table is provided.) An unusual and perhaps biochemically important feature of Zn coordination with carboxylate seen in the CSD examples is also clearly present in metalloprotein structures. With metals like Ca, carboxylate coordination is monodentate or bidentate (two M—O bonds of nearly equal length). In Zn carboxylates a continuous range between monodentate and bidentate coordination is found, with one Zn—O bond of normal length and another of any length between this and a van der Waals contact.
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    Purification, crystallization and preliminary X-ray diffraction of anthocyanidin synthase from Arabidopsis thaliana (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 425-427 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Anthocyanidin synthase (ANS) from Arabidopsis thaliana is a non-haem iron(II)-dependent dioxygenase reported to catalyse the conversion of leucoanthocyanidins to anthocyanidins. Anthocyanidins are precursors of anthocyanins, which are a major family of pigments in higher plants. ANS was crystallized by the vapour-diffusion method using polyethylene glycol as a precipitant. The crystals belong to the orthorhombic space group P212121, with unit-cell parameters a = 61.0, b = 73.2, c = 87.0 Å, and diffract to 2.4 Å using Cu Kα radiation.
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    Crystallization and preliminary X-ray crystallographic analysis of RNase HIII from Bacillus subtilis (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 438-440 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The genome of Bacillus subtilis contains three different genes encoding RNase H homologs: RNases HI, HII and HIII. RNase HIII from B. subtilis degrades RNA in RNA–DNA hybrids in an Mg2+-dependent manner like Escherichia coli RNase HI. However, they belong to different classes; the former belongs to the `class II' or `large' RNase H family, while the latter belongs to the `class I' or `small' RNase H family. RNase HIII of B. subtilis has been overexpressed in E. coli and crystallized at 296 K using sodium formate as a precipitant. The native X-ray diffraction data have been collected to 2.8 Å resolution using synchrotron radiation. The crystals are hexagonal, belonging to the space group P61, with unit-cell parameters a = b = 86.89, c = 214.49 Å, α = β = 90.0, γ = 120.0°. A self-rotation function calculation indicated the presence of two monomers of the recombinant RNase HIII in the crystallographic asymmetric unit, giving a VM of 3.43 Å3 Da−1 and a solvent content of 64.2%.
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    Purification, crystallization and preliminary X-ray diffraction analysis of the fructose-1,6-/sedoheptulose-1,7-bisphosphatase of Synechococcus PCC 7942 (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 454-456 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Fructose-1,6-/sedoheptulose-1,7-bisphosphatase of Synechococcus PCC 7942, overexpressed from Escherichia coli, has been purified and crystallized by the hanging-drop vapour-diffusion method using ammonium sulfate as a precipitant. The crystals were monoclinic, with unit-cell parameters a = 80.1, b = 84.2, c = 104.3 Å, β = 101.7°. They belonged to space group P21 and diffracted to at least 2.2 Å resolution. The calculated VM value, based on a tetramer in the asymmetric unit, was 2.2 Å3 Da−1.
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    Preliminary X-ray diffraction studies of the transcriptional inhibitory antibody Fab41.4 (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 462-464 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The binding of transcription factor ATF-1 to DNA contributes to gene expression and regulation of cell growth. Antibody Mab41.4, raised against ATF-1, and its derivatives Fab41.4 and scFv41.4 inhibit specific DNA binding in vitro and induce apoptotic death of tumor cells in vivo. Structural studies of Fab41.4 were performed to gain insight into the mechanism of action of this potentially therapeutic antibody. The optimal conditions for crystallization of Fab41.4 were determined. Crystals were needle-like in appearance, displayed C2 space-group symmetry and diffracted to a resolution of 1.6 Å. The unit-cell parameters were determined to be a = 186.64, b = 40.22, c = 55.58 Å, α = γ = 90, β = 96.93°. The data set was 97.7% complete. Molecular replacement was performed, resulting in an R value of 44.6%.
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    Perspectives in structural biology. Edited by M. Vijayan, N. Yathindra & A. S. Kolaskar. Hyderabad: Universities Press (India) Ltd, 2000. Pp. xv + 746. ISBN 81 7371 254 9. (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 477-477 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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    Crystallization of Clonorchis sinensis 26 kDa glutathione S-transferase and its fusion proteins with peptides of different lengths (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 579-581 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A Clonorchis sinensis 26 kDa glutathione S-transferase (CsGST) and its fusion proteins containing 14 and 48 amino-acid peptides at the N-terminus have been crystallized using polyethylene glycol monomethylether 550 as a precipitant. Crystals of the three proteins show very similar crystal properties: they diffract to at least 2.3 Å resolution and belong to the orthorhombic space group P212121. The unit-cell parameters of CsGST crystals were a = 66.64 (1), b = 68.91 (1), c = 123.41 (2) Å, which are very close to those of the crystals of the two fusion proteins. In addition, CsGST fusion proteins containing varying extents of N-terminal-extended peptides are incorporated into a crystal, indicating that the extended peptides have little effect on crystal packing. These results suggest that the crystallization system of CsGST/peptide fusion protein may be generally applicable to obtain crystals of small peptides.
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    Crystallization and preliminary X-ray crystallographic analysis of the human type 3 3α-hydroxysteroid dehydrogenase at 1.8 Å resolution (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 589-591 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: In androgen-sensitive target tissues, 3α-hydroxysteroid dehydrogenase regulates the androgen receptor (AR) activity by catalyzing the inactivation of 5α-dihydrotestosterone (the most natural potent androgen) to 5α-androstane-3α,17β-diol. In this report, the crystallization of a human prostatic type 3 3α-hydroxysteroid dehydrogenase, a member of the aldo–keto reductase superfamily, is described. Two different crystal forms of the complex between the human type 3 3α-HSD, NADP+ and testosterone have been obtained using PEG as precipitant. Crystal form I, which diffracts to 1.6 Å, belongs to the monoclinic space group P21, with unit-cell parameters a = 55.07, b = 87.15, c = 76.88 Å, β = 107.37° and two subunits in the asymmetric unit. A complete data set has been collected at 1.8 Å. Crystal form II, which diffracts to 2.6 Å, belongs to the rhombohedral space group R32, with unit-cell parameters a = b = 143.59, c = 205.86 Å, α = β = 90, γ = 120° and two subunits in the asymmetric unit.
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    Crystallization and functional analysis of a soluble deglycosylated form of the human costimulatory molecule B7-1 (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 605-608 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The interactions of B7-1 with CD28 and CTLA-4 modulate the course of human immune responses, making B7-1 an important target for developing structure-based therapeutics. B7-1 is, however, one of the most heavily glycosylated proteins found at the leukocyte cell surface, complicating the structural analysis of this molecule. Methods for the production, crystallization and selenomethionine labelling of a soluble deglycosylated form of this molecule are described. The protein readily forms both tetragonal plate and bipyramidal crystals belonging to space groups I4122, with unit-cell parameters a = b = 56.9, c = 298.7 Å, and P4122 (or P4322), with unit-cell parameters a = b = 89.0, c = 261.9 Å, respectively. The I4122 and primitive crystal forms diffract to 2.7 and 3.5 Å, respectively. Surface plasmon resonance-based assays indicate that the ligand-binding properties of sB7-1 are unaffected by deglycosylation. Since none of the methods relied on any special structural properties of sB7-1, it is proposed that this novel combination of procedures could in principle be adapted to the systematic analysis of many other glycoproteins of structural or functional interest.
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    Crystallization and preliminary X-ray diffraction studies of the guanylate kinase-like domain of PSD-95 protein from rat (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 616-617 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The PSD-95 (postsynaptic density-95) protein, one of the members of the MAGUK (membrane-associated guanylate kinase) family, is composed of three PDZ domains, one SH3 domain and one guanylate kinase-like (GK) domain. The GK domain mediates the scaffolding function of PSD-95 by protein–protein interaction. Here, the GK domain was subcloned, expressed as an intein fusion protein, purified without the intein and then crystallized at room temperature by the hanging-drop vapour-diffusion method using PEG 8000 as a precipitant. The complete native data set was collected to a resolution of 2.35 Å using flash-cooling. The crystals belong to the primitive tetragonal space group P43 (or P41), with unit-cell parameters a = b = 70.03 (4), c = 37.64 (1) Å.
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    On the routine use of soft X-rays in macromolecular crystallography (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 689-695 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A diffraction data set has been collected from a blood coagulation factor XIII–Ca2+ complex crystal at the X-ray diffraction beamline of the ELETTRA synchrotron (Trieste, Italy) at a wavelength of 2.6 Å. The data collection could be carried out using the beamline as is, without making any time-consuming changes to the apparatus. Various data-processing schemes have been employed and it has been observed that local or detector scaling procedures are essential for producing the `best' anomalous differences.
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    Crystallization and preliminary X-ray analysis of cardiotoxic phospholipase A2 from Ophiophagus hannah (king cobra) (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 709-710 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: An acidic phospholipase A2 exhibiting cardiotoxicity, myotoxicity and anti-platelet activity was isolated from Ophiophagus hannah (king cobra) from Guangxi, China. It contains an unusual `pancreatic loop'. The enzyme was purified to homogeneity and crystallized using polyethylene glycol and ethylene glycol as precipitants. The crystal belongs to space group C2, with unit-cell parameters a = 117.92, b = 62.94, c = 57.16 Å, β = 100.93°. Diffraction data were collected to 2.6 Å.
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    Crystallization and preliminary X-ray diffraction studies of a novel alkaline serine protease (KP-43) from alkaliphilic Bacillus sp. strain KSM-KP43 (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 717-718 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A novel alkaline serine protease (KP-43) which belongs to a new class of the subtilisin superfamily was crystallized by the sitting-drop vapour-diffusion method with ammonium sulfate as a precipitant. The crystals belong to the orthorhombic space group C2221, with unit-cell parameters a = 43.50 (2), b = 110.4 (1), c = 168.9 (1) Å. The crystals diffract X-rays beyond 1.9 Å resolution using Cu Kα radiation from a rotating-anode generator and are suitable for high-resolution crystal structure analysis.
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    Crystallization and preliminary X-ray crystallographic analysis of Escherichia coli RbsD, a component of the ribose-transport system with unknown biochemical function (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 728-730 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The Escherichia coli high-affinity ribose-transport system consists of six proteins encoded by the rbs operon (rbsD, rbsA, rbsC, rbsB, rbsK and rbsR). Of the six components, RbsD is the only one whose function is unknown. In order to gain insights into the function of RbsD by structural analysis, we overexpressed and crystallized the protein as a first step toward this goal. RbsD was overexpressed in E. coli and crystallized using the hanging-drop vapour-diffusion method at 296 K. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 285.9, b = 92.3, c = 93.3 Å, β = 105.0°. The unit cell is likely to contain 64 molecules of RbsD, with a crystal volume per protein mass (VM) of 2.43 Å3 Da−1 and a solvent content of about 49.3% by volume. An equilibrium centrifugation analysis demonstrated that RbsD (MW = 15 292 Da) exists as an octamer in solution, suggesting that the asymmetric unit contains two octameric assemblies of RbsD. A native data set to 2.7 Å resolution was obtained from a flash-cooled crystal.
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    Purification, crystallization and preliminary X-ray investigation of the complex of human vitamin D binding protein and rabbit muscle actin (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 740-742 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The vitamin D binding protein binds globular actin with high affinity and is involved in the clearance of actin from the blood circulation. A complex of the human vitamin D binding protein and rabbit muscle actin was subjected to purification steps. The pure complex was crystallized using the hanging-drop vapour-diffusion procedure. The best obtained crystals belong to the monoclinic space group P21, with unit-cell parameters a = 74.44, b = 74.90, c = 88.02 Å, β = 110.19°. A complete data set to 2.4 Å was collected from a single crystal using synchrotron radiation at DESY, Hamburg, Germany.
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    How the CO in myoglobin acquired its bend: lessons in interpretation of crystallographic data (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 751-754 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Contrary to the expectation of chemists, the first X-ray structures of carbon monoxide bound to myoglobin (Mb) showed a highly distorted Fe—C—O bond system. These results appeared to support the idea of a largely steric mechanism for discrimination by the protein against CO binding, a lethal act for the protein in terms of its physiological function. The most recent independently determined high-resolution structures of Mb–CO have allowed the 25 year old controversy concerning the mode of CO binding to be resolved. The CO is now seen to bind in a roughly linear fashion without substantial bending, consistent with chemical expectations and spectroscopic measurements. Access to deposited diffraction data prompted a reevaluation of the sources of the original misinterpretation. A series of careful refinements of models against the data at high (1.1 Å) and modest resolutions (1.5 Å) have been performed in anisotropic versus isotropic modes. The results suggest that the original artifact was a result of lower quality crystals combined with anisotropic motion and limited resolution of the diffraction data sets. This retrospective analysis should serve as a caution for all researchers using structural tools to draw far-reaching biochemical conclusions.
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    Post-translational modification of the N-terminal His tag interferes with the crystallization of the wild-type and mutant SH3 domains from chicken src tyrosine kinase (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 759-762 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Structural studies of the wild type and mutants of the src SH3 domain were initiated to elucidate the correlation of the native-state topology with protein thermostability and folding kinetics. An extra mass of 178 Da arising from the post-translational modification at the N-terminal His tag was observed. The spontaneous α-N-6 gluconoylation at the amino group of the His-tagged SH3 domain contributed to the observed extra mass. The partial modification of the N-terminal His-tag produced heterogeneity, both in size and in charge, in the Escherichia coli expressed SH3 domain. The removal of the His tag from the SH3 domain was essential for the crystallization of both wild-type and mutant src SH3. Both the wild type and the W43I mutant were crystallized by hanging-drop vapor diffusion and are in the hexagonal space group P6522 with one molecule in the asymmetric unit. Data sets were collected to 1.8 and 1.95 Å resolution for the the wild type and the W43I mutant, respectively.
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    Effects of different post-crystallization soaking conditions on the diffraction of Mtcp1 crystals (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 763-765 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of human Mtcp1 was determined at 2 Å resolution after the X-ray diffraction limit was improved by post-crystallization soaking in 2.0 M ammonium sulfate for 1–5 months. The effects of varying the ammonium sulfate concentration and addition of polyethylene glycol to the soaking solution were examined in order to understand the phenomenon and to reduce the soaking time. Soaking the crystal for one week in a solution of 1.5 M ammonium sulfate and 2% PEG 3400 gave the desired improvement in diffraction quality. Therefore, different soaking conditions should be explored when crystals show disordered and low-resolution diffraction.
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    Structure of the N-terminal domain of Yersinia pestis YopH at 2.0 Å resolution (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 793-799 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Yersinia pestis, the causative agent of bubonic plague, injects effector proteins into the cytosol of mammalian cells that enable the bacterium to evade the immune response of the infected organism by interfering with eukaryotic signal transduction pathways. YopH is a modular effector composed of a C-terminal protein tyrosine phosphatase (PTPase) domain and a multifunctional N-terminal domain that not only orchestrates the secretion and translocation of YopH into eukaryotic cells but also binds tyrosine-phosphorylated target proteins to mediate substrate recognition. The crystal structure of the N-terminal domain of YopH (YopHN; residues 1–130) has been determined at 2.0 Å resolution. The amino-acid sequences that target YopH for secretion from the bacterium and translocation into eukaryotic cells form integral parts of this compactly folded domain. The structure of YopHN bears no resemblance to eukaryotic phosphotyrosine-binding domains, nor is it reminiscent of any known fold. Residues that have been implicated in phosphotyrosine-dependent protein binding are clustered together on one face of YopHN, but the structure does not suggest a mechanism for protein–phosphotyrosine recognition.
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    Checking nucleic acid crystal structures (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 813-828 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The program SFCHECK [Vaguine et al. (1999), Acta Cryst. D55, 191–205] is used to survey the quality of the structure-factor data and the agreement of those data with the atomic coordinates in 105 nucleic acid crystal structures for which structure-factor amplitudes have been deposited in the Nucleic Acid Database [NDB; Berman et al. (1992), Biophys. J. 63, 751–759]. Nucleic acid structures present a particular challenge for structure-quality evaluations. The majority of these structures, and DNA molecules in particular, have been solved by molecular replacement of the double-helical motif, whose high degree of symmetry can lead to problems in positioning the molecule in the unit cell. In this paper, the overall quality of each structure was evaluated using parameters such as the R factor, the correlation coefficient and various atomic error estimates. In addition, each structure is characterized by the average values of several local quality indicators, which include the atomic displacement, the density correlation, the B factor and the density index. The latter parameter measures the relative electron-density level at the atomic position. In order to assess the quality of the model in specific regions, the same local quality indicators are also surveyed for individual groups of atoms in each structure. Several of the global quality indicators are found to vary linearly with resolution and less than a dozen structures are found to exhibit values significantly different from the mean for these indicators, showing that the quality of the nucleic acid structures tends to be rather uniform. Analysis of the mutual dependence of the values of different local quality indicators, computed for individual residues and atom groups, reveals that these indicators essentially complement each other and are not redundant with the B factor. Using several of these indicators, it was found that the atomic coordinates of the nucleic acid bases tend to be better defined than those of the backbone. One of the local indicators, the density index, is particularly useful in spotting regions of the model that fit poorly in the electron density. Using this parameter, the quality of crystallographic water positions in the analyzed structures was surveyed and it was found that a sizable fraction of these positions have poorly defined electron density and may therefore not be reliable. The possibility that cases of poorly positioned water molecules are symptomatic of more widespread problems with the structure as a whole is also raised.
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    Optimization of Met8p crystals through protein-storage buffer manipulation (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 867-869 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Sirohaem, the prosthetic group of assimilatory sulfite and nitrite reductases, is a modified tetrapyrrole that belongs to the same fraternity of metallo-prosthetic groups as haem, chlorophyll, cobalamin and coenzyme F430 [Warren & Scott (1990), Trends Biochem Sci. 15, 486–491]. In Saccharomyces cerevisiae, the last step in the biosynthesis of sirohaem involves Met8p, a bifunctional enzyme responsible for both the NAD+-dependent dehydrogenation of the corrin ring and ferrochelation. Optimization of the protein storage buffer according to the results of crystallization trials resulted in a more monodisperse protein solution. Crystals were grown that diffracted to 2.1 Å.
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    Crystallization and preliminary X-ray diffraction analysis of NADP-dependent glyceraldehyde-3-phosphate dehydrogenase of SynechococcusPCC 7942 (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 879-881 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPDH) of Synechococcus PCC 7942 was crystallized in two different forms by the hanging-drop vapour-diffusion method using ammonium sulfate as a precipitant. Form I crystals were hexagonal, space group P65 or P61, with unit-cell parameters a = b = 91.1, c = 428.6 Å, γ = 120°. Form II crystals were monoclinic, space group C2, with unit-cell parameters a = 152.3, b = 80.9, c = 213.6 Å, β = 103.1°. Native data were collected from a frozen crystal of form I to a resolution of 2.8 Å using synchrotron radiation at SPring-8, whereas form II crystals were easily damaged by radiation at room temperature and increased mosaicity in cryoprotectant solutions. A molecular-replacement solution of the form I crystal was obtained in space group P65 using the program AMoRe and the structure of the NAD-dependent GAPDH from Bacillus stearothermophilus.
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    Crystallographic characterization of the radixin FERM domain bound to the cytoplasmic tail of the adhesion protein ICAM-2 (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 891-892 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Radixin is a member of the ERM proteins, which cross-link plasma membranes and actin filaments. The FERM domains located at the N-terminal regions of ERM proteins are responsible for membrane association through direct interactions with the cytoplasmic domains of integral membrane proteins. Here, crystals of the complex between the radixin FERM domain and the full-length cytoplasmic tail (28-residue peptide) of intercellular adhesion molecule 2, ICAM-2, have been obtained. The crystals were found to belong to space group P3121 or P3221, with unit-cell parameters a = b = 100.44 (9), c = 99.49 (6) Å, and contain one complex in the crystallographic asymmetric unit. An intensity data set was collected to a resolution of 2.60 Å.
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    Crystallization and preliminary X-ray analysis of the complex between human CTLA-4 and B7-2 (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 898-899 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: CTLA-4 is a dimeric T-cell surface receptor responsible for transducing signals that down-regulate activated T cells upon binding B7 ligands. The disulfide-linked homodimer of the extracellular segment of human CTLA-4 and the receptor-binding domain of human B7-2 were purified and cocrystallized. Diffraction from these crystals is consistent with the monoclinic space group P21 (unit-cell parameters a = 47.85, b = 54.56, c = 103.09 Å, β = 91.63); native data have been collected to 3.2 Å resolution.
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    Cloning, expression, purification and preliminary X-ray crystallographic studies of Escherichia coli Hsp100 ClpB nucleotide-binding domain 1 (NBD1) (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 909-911 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Escherichia coli Hsp100 ClpB plays critical roles in multi-chaperone systems in cell physiology. After being activated by protein or peptide binding, ClpB disaggregates denatured polypeptides by employing ATP hydrolysis and allows other molecular chaperones such as Hsp70 DnaK and Hsp40 DnaJ to refold the non-native polypeptides. ClpB contains two nucleotide-binding domains with Walker A and B motifs within their primary sequences. Therefore, ClpB can be classified as a member of the large ATPase family known as ATPases associated with various cellular activities (AAAs). The mechanisms by which the ClpB acts as a molecular chaperone to disaggregate denatured polypeptides are unknown. To investigate how the nucleotide-binding domain participates in ClpB chaperone activity, we have cloned and crystallized ClpB nucleotide-binding domain 1 (NBD1). The ClpB NBD1 crystals diffract to 1.80 Å using a synchrotron X-ray source and belong to the space group P212121, with unit-cell parameters a = 38.41, b = 65.48, c = 79.13 Å. Structure determination by the MAD method is under way.
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    Structure of aspergillopepsin I from Aspergillus phoenicis: variations of the S1′–S2 subsite in aspartic proteinases (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 948-956 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of aspergillopepsin I (AP) from Aspergillus phoenicis has been determined at 2.18 Å resolution and refined to R and Rfree factors of 21.5 and 26.0%, respectively. AP has the typical two β-barrel domain structure of aspartic proteinases. The structures of the two independent molecules are partly different, exemplifying the flexible nature of the aspartic proteinase structure. Notably, the `flap' in one molecule is closer, with a largest separation of 4.0 Å, to the active site than in the other molecule. AP is most structurally homologous to penicillopepsin (PP) and then to endothiapepsin (EP), which share sequence identities of 68 and 56%, respectively. However, AP is similar to EP but differs from PP in the combined S1′–S2 subsite that is delineated by a flexible ψ-loop in the C-terminal domain. The S1′ and S2 subsites are well defined and small in AP, while there is no definite border between S1′ and S2 and the open space for the S2 subsite is larger in PP. Comparison of the structures indicates that the two amino-acid residues equivalent to Leu295 and Leu297 of AP are the major determining factors in shaping the S1′–S2 subsite in the fungal aspartic proteinases.
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    High-resolution neutron structure of nicotinamide adenine dinucleotide (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 981-989 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of the free-acid form of the coenzyme NAD+ was determined at 100 K from a single-crystal neutron experiment. NAD+ is the oxidized form of the coenzyme redox pair NAD+/NADH and plays an important role in the catalysis of biological processes. The molecule crystallizes in space group P1 with one NAD+ and four water molecules per unit cell. The structure is compared with the previous X-ray models of NAD+ [Reddy et al. (1981), J. Am. Chem. Soc. 103, 907–914; Parthasarathy & Fridey (1984b), Science, 226, 969–971; Guillot et al. (2000), Acta Cryst. C56, 726–728]. The crystal packing and the hydrogen-bond pattern are discussed as well as four short C—H\cdotsO contacts involving the pyridine and adenine rings. The structure displays stereochemical distortions owing to the hydrogen bonding and crystal-packing constraints, reflecting the adaptability of the NAD+ molecule in various chemical environments.
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    Using surface-bound rubidium ions for protein phasing (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1008-1012 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Rubidium is a monovalent metal that can be used as a counterion in protein solutions. X-ray anomalous scattering from rubidium ions bound to the protein surface was used for phasing of the crystal structure of the hsp60 apical domain from Thermus thermophilus. Multiple-wavelength anomalous dispersion (MAD) data were collected from a crystal obtained from a solution containing 0.2 M rubidium salt. One molecule of protein (147 amino acids) binds one well ordered and one poorly ordered Rb atom. Phases calculated with the program SHARP were sufficient for automatic tracing and side-chain assignment using the program ARP/wARP. The data show that bound rubidium ions can be used to determine protein structures and to study the interaction of monovalent metal ions with proteins and other macromolecules.
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    Crystallization and preliminary X-ray analysis of UDP-N-acetylenolpyruvylglucosamine reductase (MurB) from Staphylococcus aureus (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1032-1035 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: UDP-N-acetylenolpyruvylglucosamine reductase (MurB) is an essential enzyme in the bacterial cell-wall biosynthetic pathway, making it a potential therapeutic target for novel antibiotics. Diffraction-quality crystals of both the native and Se-methionine-expressed MurB from Staphylococcus aureus have been prepared by sitting-drop vapour diffusion from solutions containing polyethylene glycol (PEG) 8000, ammonium sulfate, sodium cacodylate pH 6.5 and dimethyl sulfoxide (DMSO). Crystals belong to the cubic space group I213, with unit-cell parameters a = b = c = 178.99 Å. X-ray data from these crystals were collected at the Advanced Photon Source 17-ID beamline and were used to solve the MurB structure to 2.3 Å resolution.
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    Structure of rat transthyretin (rTTR) complex with thyroxine at 2.5 Å resolution: first non-biased insight into thyroxine binding reveals different hormone orientation in two binding sites (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1061-1070 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The first observation of the unique environment for thyroxine (T4) binding in tetrameric rat transthyretin (rTTR) is reported as determined by X-ray diffraction. These data revealed different modes of hormone binding in the two unique hormone-binding sites in the rat TTR tetramer channel. Differences in the orientation of thyroxine and the position of water molecules in the two binding sites further suggest a mechanism for the docking pathway of the hormone into the channel of TTR. Crystals of the rat transthyretin–thyroxine complex are isomorphous with those reported for apo rTTR and crystallized in the tetragonal space group P43212 with four independent TTR monomeric subunits in the asymmetric part of the crystal lattice. Data were collected to 2.5 Å resolution and the structure was refined to R = 20.9% for 15 384 data in the resolution range 12–2.5 Å. Similar to human TTR, the rat protein is also a 54 000 Da tetramer with four identical polypeptide chains of 127 amino-acid residues. Of the 22 amino-acid residues which differ between the human and rat sequences, none are in the thyroxine-binding domains. Analysis of these structural data reveals that the tertiary structure is similar to that of hTTR, with only small differences in the flexible loop regions on the surface of the structure. Conformational changes of the amino acids in the channel result in a hydrogen-bonded network that connects the two binding domains, in contrast to the hydrogen bonds formed along the tetramer interface in the apo transthyretin structure. These changes suggest a mechanism for the signal transmission between thyroxine-binding domains.
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    Structure of the insecticidal bacterial δ-endotoxin Cry3Bb1 of Bacillus thuringiensis (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1101-1109 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The coleopteran-active δ-endotoxin Cry3Bb1 from Bacillus thuringiensis (Bt) strain EG7231 is uniquely toxic to Diabrotica undecimpunctata, the Southern corn rootworm, while retaining activity against Leptinotarsa decemlineata, the Colorado potato beetle. The crystal structure of the δ-endotoxin Cry3Bb1 has been refined using data collected to 2.4 Å resolution, with a residual R factor of 17.5% and an Rfree of 25.3%. The structure is made up of three domains: I, a seven-helix bundle (residues 64–294); II, a three-sheet domain (residues 295–502); and III, a β-sandwich domain (residues 503–652). The monomers in the orthorhombic C2221 crystal lattice form a dimeric quaternary structure across a crystallographic twofold axis, with a channel formed involving interactions between domains I and III. There are 23 hydrogen bonds between the two monomers conferring structural stability on the dimer. It has been demonstrated that Cry3Bb1 and the similar toxin Cry3A form oligomers in solution. The structural results presented here indicate that the interactions between domains I and III could be responsible for the initial higher order structure and have implications for the biological activity of these toxins. There are seven additional single amino-acid residues in the sequence of Cry3Bb1 compared with that of Cry3A; one in domain I, two in domain II and four in domain III, which also shows the largest conformational difference between the two proteins. These changes can be implicated in the selectivity differences noted for these two δ-endotoxins.
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    Crystals of a mutant form of ribosomal protein L22 rendering bacterial ribosomes resistant to erythromycin (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1150-1152 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A mutant form of Thermus thermophilus ribosomal protein L22 responsible for erythromycin resistance has been overexpressed in Escherichia coli, purified to homogeneity and crystallized using the hanging-drop vapour-diffusion technique. While several different crystallization conditions were found, only one set of conditions yielded crystals suitable for X-ray diffraction analysis. These crystals grow as thick plates, with unit-cell parameters a = 31.8, b = 86.59, c = 38.96 Å, β = 104.47°. The crystals belong to the space group P21 and diffract to 1.8 Å resolution. On the basis of density calculations, two monomers are predicted per asymmetric unit (VM = 2.06 Å3 Da−1), with a solvent content of 40%.
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    Crystallization and preliminary X-ray crystallographic studies of recombinant thermoresistant gluconate kinase GntK from Escherichia coli (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1159-1161 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The thermoresistant gluconate kinase GntK from Escherichia coli, an essential enzyme in gluconate metabolism, has been expressed, purified and crystallized. For crystallization, the hanging-drop vapour-diffusion method was used with polyethylene glycol (PEG) 6000 and lithium chloride as precipitants. Three crystal forms belonging to the monoclinic space group C2 or the orthorhombic space groups P212121 and P21212 were obtained. The unit-cell parameters are a = 75.0, b = 79.3, c = 70.2 Å, β = 105.3° (C2), a = 52.0, b = 79.3, c = 89.8 Å (P212121) and a = 70.1, b = 74.1, c = 78.9 Å (P21212). In all three crystal forms, there are two molecules in the asymmetric unit; the different forms occur in the same crystallization drop. The crystals diffract to at least 2.0 Å using synchrotron radiation.
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    Expression, purification, crystallization and preliminary X-ray diffraction analysis of the human calcium-binding protein MRP14 (S100A9) (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1174-1176 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: MRP14 is a protein that is specifically expressed in myeloid and epithelial cells during the stages of acute or chronic inflammatory states such as rheumatoid arthritis or sarcoidosis. MRP14 has EF-hand motifs as Ca2+-binding sites and belongs to the S100 family of proteins. This paper deals with the sample preparation (cloning, overexpression and purification), crystallization and preliminary crystallographic analysis of recombinant human MRP14. Crystals of MRP14 were obtained by the hanging-drop vapour-diffusion method. MRP14 crystals belong to space group P21, with unit-cell parameters a = 57.59, b = 178.44, c = 61.23 Å, β = 113.17°, and diffract to 2.1 Å resolution.
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    Crystallization and preliminary X-ray analysis of clade I catalases from Pseudomonas syringae and Listeria seeligeri (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1184-1186 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Haem-containing catalases are homotetrameric molecules that degrade hydrogen peroxide. Phylogenetically, the haem-containing catalases can be grouped into three main lines or clades. The crystal structures of seven catalases have been determined, all from clades II and III. In order to obtain a structure of an enzyme from clade I, which includes all plant, algae and some bacterial enzymes, two bacterial catalases, CatF from Pseudomonas syringae and Kat from Listeria seeligeri, have been crystallized by the hanging-drop vapour-diffusion technique, using PEG and ammonium sulfate as precipitants, respectively. Crystals of P. syringae CatF, with a plate-like morphology, belong to the monoclinic space group P21, with unit-cell parameters a = 60.6, b = 153.9, c = 109.2 Å, β = 102.8°. From these crystals a diffraction data set to 1.8 Å resolution with 98% completeness was collected using synchrotron radiation. Crystals of L. seeligeri Kat, with a well developed bipyramidal morphology, belong to space group I222 (or I212121), with unit-cell parameters a = 74.4, b = 121.3, c = 368.5 Å. These crystals diffracted beyond 2.2 Å resolution when using synchrotron radiation, but presented anisotropic diffraction, with the weakest direction perpendicular to the long c axis.
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    Structure of human muscle creatine kinase (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1196-1200 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of human muscle creatine kinase has been determined by the molecular-replacement method and refined at 3.5 Å resolution. The structures of both the monomer and the dimer closely resemble those of the other known structures in the creatine kinase family. Two types of dimers, one with a non-crystallographic twofold symmetry axis and the other with a crystallographic twofold symmetry axis, were found to occur simultaneously in the crystal. These dimers form an infinite `double-helix'-like structure along an unusual long crystallographic 31 axis.
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    Structure of lobster apocrustacyanin A1 using softer X-rays (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1219-1229 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The molecular basis of the camouflage colouration of marine crustacea is often provided by carotenoproteins. The blue colour of the lobster carapace, for example, is intricately associated with a multimacromolecular 16-mer complex of protein subunits each with a bound astaxanthin molecule. The protein subunits of crustacyanin fall into two distinct subfamilies, CRTC and CRTA. Here, the crystal structure solution of the A1 protein of the CRTC subfamily is reported. The problematic nature of the structure solution of the CRTC proteins (both C1 and A1) warranted consideration and the development of new approaches. Three putative disulfides per protein subunit were likely to exist based on molecular-homology modelling against known lipocalin protein structures. With two such subunits per crystallographic asymmetric unit, this direct approach was still difficult as it involved detecting a weak signal from these sulfurs and suggested the use of softer X-rays, combined with high data multiplicity, as reported previously [Chayen et al. (2000), Acta Cryst. D56, 1064–1066]. This paper now describes the structure solution of CRTC in the form of the A1 dimer based on use of softer X-rays (2 Å wavelength). The structure solution involved a xenon derivative with an optimized xenon LI edge f'' signal and a native data set. The hand of the xenon SIROAS phases was determined by using the sulfur anomalous signal from a high-multiplicity native data set also recorded at 2 Å wavelength. For refinement, a high-resolution data set was measured at short wavelength. All four data sets were collected at 100 K. The refined structure to 1.4 Å resolution based on 60 276 reflections has an R factor of 17.7% and an Rfree of 22.9% (3137 reflections). The structure is that of a typical lipocalin, being closely related to insecticyanin, to bilin-binding protein and to retinol-binding protein. This A1 monomer or dimer can now be used as a search motif in the structural studies of the oligomeric forms α- and β-crustacyanins, which contain bound astaxanthin molecules.
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    Overexpression, purification, crystallization and data collection of a single-stranded DNA-binding protein from Sulfolobus solfataricus (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1290-1292 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Single-stranded DNA-binding proteins are recruited when single-stranded DNA is exposed by disruption of the duplex. Many important biological processes such as DNA replication can only occur when the two strands of the duplex are separated. A defining trait of these proteins is the presence of the so-called OB fold. The single-stranded DNA-binding protein of the crenarchaeote Sulfolobus solfataricus has a number of interesting differences and similarities to both the eubacterial and eukaryotic homologues. It has an extended C-terminal tail with significant sequence identity to a similar region in the eubacterial protein. However, the sequence of the OB fold is much more like the eukaryotic and euryarchaeal proteins. The S. solfataricus protein remains a monomer in the absence of DNA but rapidly polymerizes upon binding – a behaviour not seen in the Escherichia coli protein. The protein has been overexpressed, purified and crystallized. The protein crystallizes in two related forms, both having space group P61 (or P65) with approximate unit-cell parameters a = b = 75, c = 69 Å, but the crystals are distinguished by their size and morphology. The larger crystals are hexagonal bipyramids and are merohedrally twinned, diffracting to 1.34 Å with diffraction observed to 1.2 Å. Smaller needle-like crystals diffract to about 2.0 Å but are not twinned. Molecular-replacement attempts have failed owing to low identity with available search models. The structure will be determined by multiple-wavelength methods.
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    Crystallization and preliminary crystallographic analysis of the recombinant N-terminal domain of riboflavin synthase (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1296-1299 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Riboflavin synthase catalyzes the final step in the biosynthesis of riboflavin. Animals and humans lack this enzyme, whereas many bacteria and certain yeasts are absolutely dependent on endogenous riboflavin synthesis. Riboflavin synthase is therefore an attractive target for chemotherapy. The N-terminal domain of riboflavin synthase forms a dimer in solution and is capable of strongly binding riboflavin. It can serve as a model for the binding site of the native enzyme. Structural information obtained from this domain at high resolution will be helpful in the determination of the binding mode of riboflavin and thus for the development of antimicrobial drugs. Here, the crystallization and preliminary crystallographic analysis of the N-terminal domain of riboflavin synthase are reported. The crystals belong to the space group C2221, with unit-cell parameters a = 50.3, b = 104.7, c = 85.3 Å, α = β = γ = 90°, and diffract to 2.6 Å resolution.
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    Crystallization and preliminary X-ray diffraction analysis of a novel trypsin inhibitor from seeds of Copaifera langsdorffii (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1316-1318 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A novel trypsin inhibitor isolated from seeds of Copaifera langsdorffii was purified to homogeneity and crystallized. Crystals suitable for X-ray analysis were grown using the hanging-drop vapour-diffusion method at 291 K in sodium acetate buffer at pH values near 4.3 using PEG 4000 as precipitant. The crystals presented symmetry compatible with the space group P41212 or P43212, with unit-cell parameters a = b = 58.71, c = 93.75 Å, and diffracted to 1.83 Å resolution at the synchrotron source.
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    Crystallization and preliminary X-ray analysis of a depressant insect toxin from the scorpion Buthus martensii Karsch (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1313-1315 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Depressant insect toxins are a distinct group of scorpion neurotoxins for which no three-dimensional structures are yet available. A depressant insect toxin named BmK dITAP3 from the scorpion Buthus martensii Karsch (BmK) has been purified and crystallized. Single crystals of dITAP3 grew in the presence of the detergent CYMAL-6 using the hanging-drop vapour-diffusion method with ammonium sulfate as precipitant. A set of diffraction data to 2.6 Å resolution has been collected. Preliminary analysis of the diffraction data indicated that the crystal belonged to space group R3, with unit-cell parameters a = b = 73.29, c = 68.90 Å, α = β = 90, γ = 120°. Assuming two molecules in the asymmetric unit, the estimated solvent content is 53.4%.
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    Solution solution: using NMR models for molecular replacement (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1457-1461 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: NMR structures can serve as a good source of search models in crystal structure determination by molecular replacement. However, owing to the inherent problems of NMR models, this procedure is not always straightforward. Here, an updated overview is presented with particular emphasis on the preparation of NMR search models and the latest trends in methodology. An experimental protocol developed recently is described and results on its use in solving a new structure as well as its test against a difficult published case are presented.
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    Molecular replacement by evolutionary search (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1474-1479 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Stochastic search algorithms can be used to perform rapid six-dimensional molecular-replacement searches. A molecular-replacement procedure has been developed that uses an evolutionary algorithm to simultaneously optimize the orientation and position of a search model in a unit cell. Here, the performance of this algorithm and its dependence on search model quality and choice of target function are examined. Although the evolutionary search procedure is capable of finding solutions with search models that represent only a small fraction of the total scattering matter of the target molecule, the efficiency of the search procedure is highly dependent on the quality of the search model. Polyalanine models frequently provide better search efficiency than all-atom models, even in cases where the side-chain positions are known with high accuracy. Although the success of the search procedure is not highly dependent on the statistic used as the target function, the correlation coefficient between observed and calculated structure-factor amplitudes generally results in better search efficiency than does the R factor. An alternative stochastic search procedure, simulated annealing, provides similar overall performance to evolutionary search. Methods of extending the evolutionary search algorithm to include internal optimization, selection and construction of the search model are now beginning to be investigated.
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    Structure of cytochrome c2 from Rhodospirillum centenum (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1498-1505 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Cytochrome c2 from the purple photosynthetic bacterium Rhodospirillum centenum has been crystallized by the sitting-drop vapour-diffusion method. The crystals belong to the orthorhombic space group P212121, with unit-cell parameters a = 29.7, b = 59.9, c = 65.4 Å, and diffract to a resolution limit of 1.7 Å. The Fe-atom position was determined from its anomalous scattering contribution and a molecular-replacement solution was calculated. The correctness of the solution was confirmed by parallel isomorphous replacement studies. The resulting model has a type I cytochrome fold with two features, an extended α-helix and a surface-charge distribution, that are distinctive to this protein. The implications of these structural features for the ability of the cytochrome to serve as an electron carrier are discussed.
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    How to take advantage of non-crystallographic symmetry in molecular replacement: `locked' rotation and translation functions (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1383-1389 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Many protein molecules form assemblies that obey point-group symmetry. These assemblies are often situated at general positions in the unit cell such that the point-group symmetry of the assembly becomes non-crystallographic symmetry (NCS) in the crystal. The presence of NCS places significant constraints on structure determination by the molecular-replacement method. The locked rotation and translation functions have been developed to take advantage of the presence of NCS in this structure determination, which generally requires four steps. (i) The locked self-rotation function is used to determine the orientation of the NCS assembly in the crystal, relative to a pre-defined `standard' orientation of this NCS point group. (ii) The locked cross-rotation function is used to determine the orientation of one monomer of the assembly in the standard orientation. This calculation requires only the structure of the monomer as the search model. (iii) The locked translation function is used to determine the position of this monomer relative to the center of the assembly. Information obtained from steps (ii) and (iii) will produce a model of the entire assembly centered at the origin of the coordinate system. (iv) An ordinary translation function is used to determine the center of the assembly in the crystal unit cell, using as the search model the structure of the entire assembly produced in step (iii). The locked rotation and translation functions simplify the structure-determination process in the presence of NCS. Instead of searching for each monomer separately, the locked calculations search for a single rotation or translation. Moreover, the locked functions reduce the noise level in the calculation, owing to the averaging over the NCS elements, and increase the signals as all monomers of the assembly are taken into account at the same time.
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    Phasing from an envelope (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1410-1414 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Solution of the phase problem is central to crystallographic structure determination. Conventional molecular-replacement methods are ineffective in the absence of knowledge of the structure of a homologous protein. A recent method utilizing the low-resolution molecular shape determined from solution X-ray scattering data has been shown to be successful in locating the molecular shape within the crystallographic unit cell for the cases of the trimeric nitrite reductase (AxNiR, 105 kDa) and the dimeric superoxide dismutase (SOD, 32 kDa). This was achieved by performing a direct real-space search for orientation and translation using the orientation of the non-crystallographic axis obtained by performing a self-rotation on the crystallographic data. This effectively reduces the potential six-dimensional search to a four-dimensional one (Eulerian angle γ and three translational parameters). The program FSEARCH incorporating this method has been generalized to handle molecules from all space groups. The program can also be used in general six-dimensional cases for a molecular-replacement solution given a predetermined envelope from any source, such as electron-microscopic images or solution scattering, provided that the envelope can be converted to the standard CCP4 map format or expressed in terms of spherical harmonics. It is hoped that this method will greatly facilitate the ab initio structure determination of proteins and provide a good foundation for further structure refinement.
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    Molecular placement of experimental electron density: a case study on UDP-galactopyranose mutase (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1415-1420 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of UDP-galactopyranose mutase, the enzyme responsible for the conversion of UDP-galactopyranose to UDP-galactofuranose, has been solved. The structure solution required the use of two crystal forms and a selenomethionine variant. Crystal form P21 was used to collect a complete MAD data set, a native data set and a single-wavelength non-isomorphous selenomethionine data set. A starting set of MAD phases was then improved by non-crystallographic averaging and cross-crystal averaging of all P21 data. The initial maps were of such low quality that transformation matrices between cells could not be determined. It was therefore assumed that although there were large changes in unit-cell parameters, the molecule occupied the same position in each cell. This starting assumption was allowed to refine during the averaging procedure and did so satisfactorily. Despite a visible increase in the quality of the map allowing some secondary-structural elements to be located, the overall structure could not be traced and refined. The rediscovery of the second crystal form, P212121, allowed the collection of a native data set to 2.4 Å. Molecular placement of electron density was used to determine the relationship between the two unit cells. In this study, only the already averaged P21 experimental density could be placed in the P212121 map. Less extensively density-modified maps did not give a clear solution. The study suggests even poor non-isomorphous data can be used to significantly improve map quality. The relationship between P21 and P212121 could then be used in a final round of cross-crystal averaging to generate phases. The resulting map was easily traced and the structure has been refined. The structure sheds important light on a novel mechanism and is also a therapeutic target in the treatment of tuberculosis.
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    Spherically averaged phased translation function and its application to the search for molecules and fragments in electron-density maps (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1451-1456 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The molecular-replacement method has been extended to locate molecules and their fragments in an electron-density map. The approach is based on a new spherically averaged phased translation function. The position of the centre of mass of a search model is found prior to determination of its orientation. The orientation is subsequently found by a phased rotation function. The technique also allows superposition of distantly related macromolecules. The method has been implemented in a computer program MOLREP and successfully tested using experimental data sets.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901012409
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    Multidimensional molecular replacement (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1462-1473 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A method is described which attempts to simultaneously and independently determine the positional and orientational parameters of all molecules present in the asymmetric unit of a target crystal structure. This is achieved through a reverse Monte Carlo optimization of a suitable statistic (such as the R factor or the linear correlation coefficient between the observed and calculated amplitudes of the structure factors) in the 6n-dimensional space defined by the rotational and translational parameters of the n search models. Results from the application of this stochastic method – obtained with a space-group-general computer program which has been developed for this purpose – indicate that with present-day computing capabilities the method may be applied successfully to molecular-replacement problems for which the target crystal structure contains up to three molecules per asymmetric unit. It is also shown that the method may be useful in cases where the assumption of topological segregation of the self- and cross-vectors in the Patterson function is violated (as may happen, for example, in closely packed crystal structures).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901008563
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    ARP/wARP and molecular replacement (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1445-1450 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The aim of ARP/wARP is improved automation of model building and refinement in macromolecular crystallography. Once a molecular-replacement solution has been obtained, it is often tedious to refine and rebuild the initial (search) model. ARP/wARP offers three options to automate that task to varying extents: (i) autobuilding of a completely new model based on phases calculated from the molecular-replacement solution, (ii) updating of the initial model by atom addition and deletion to obtain an improved map and (iii) docking of a structure onto a new (or mutated) sequence, followed by rebuilding and refining the side chains in real space. A few examples are presented where ARP/wARP made a considerable difference in the speed of structure solution and/or made possible refinement of otherwise difficult or uninterpretable maps. The resolution range allowing complete autobuilding of protein structures is currently 2.0 Å, but for map improvement considerable advances over more conventional refinement techniques are evident even at 3.2 Å spacing.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901014007
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    Structure of Urtica dioica agglutinin isolectin I: dimer formation mediated by two zinc ions bound at the sugar-binding site (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1513-1517 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Ultica dioica agglutinin, a plant lectin from the stinging nettle, consists of a total of seven individual isolectins. One of these structures, isolectin I, was determined at 1.9 Å resolution by the X-ray method. The crystals belong to the space group P21 and the asymmetric unit contains two molecules related by local twofold symmetry. The molecule consists of two hevein-like chitin-binding domains lacking distinct secondary structure, but four disulfide bonds in each domain maintain the tertiary structure. The backbone structure of the two independent molecules is essentially identical and this is similarly true of the sugar-binding sites. In the crystal, the C-terminal domains bind Zn2+ ions at the sugar-binding site. Owing to their location near a pseudo-twofold axis, the two zinc ions link the two independent molecules in a tail-to-tail arrangement: thus, His47 of molecule 1 and His67 of molecule 2 coordinate the first zinc ion, while the second zinc ion links Asp75 of molecule 1 and His47 of molecule 2.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S090744490101232X
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    Structure at 2.6 Å resolution of phenylalanyl-tRNA synthetase complexed with phenylalanyl-adenylate in the presence of manganese (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1534-1544 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of phenylalanyl-tRNA synthetase (PheRS) from Thermus thermophilus, a class II aminoacyl-tRNA synthetase, complexed with phenylalanyl-adenylate (Phe-AMP) was determined at 2.6 Å resolution. Crystals of native PheRS were soaked in a solution containing phenylalanine and ATP in the presence of Mn2+ ions. The first step of the aminoacylation reaction proceeds within the crystals, resulting in Phe-AMP formation at the active site. Specific recognition of the phenylalanine portion of the Phe-AMP is achieved by interactions of the phenyl ring of Phe-AMP with two neighbouring residues, Pheα258 and Pheα260. No manganese ions were observed within the active site; their role in the formation of the transition state may be assigned to a number of polar residues and water molecules. In the anomalous Fourier difference map, a divalent metal ion was detected at the interface of the α- and β-subunits at a short distance from motif 3 residues participating in the substrate binding. A sulfate ion, which was identified on the protein surface, may mediate the interactions of PheRS with DNA. Visible conformational changes were detected in the active-site area adjacent to the position of the Phe-AMP, compared with the structure of PheRS complexed with a synthetic adenylate analogue (phenylalaninyl-adenylate). Based on the known structures of the substrate-free enzyme and its complexes with various ligands, a general scheme for the phenylalanylation mechanism is proposed.
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    URL: http://dx.doi.org/10.1107/S090744490101321X
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    Structure of human uropepsin at 2.45 Å resolution (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1560-1570 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The molecular structure of human uropepsin, an aspartic proteinase from the urine produced in the form of pepsinogen A in the gastric mucosa, has been determined by molecular replacement using human pepsin as the search model. Crystals belong to space group P212121, with unit-cell parameters a = 50.99, b = 75.56, c = 89.90 Å. Crystallographic refinement led to an R factor of 0.161 at 2.45 Å resolution. The positions of 2437 non-H protein atoms in 326 residues have been determined and the model contains 143 water molecules. The structure is bilobal, consisting of two predominantly β-sheet lobes which, as observed in other aspartic proteinases, are related by a pseudo-twofold axis. A model of the uropepsin–pepstatin complex has been constructed based on the high-resolution crystal structure of pepsin complexed with pepstatin.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901013865
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  • 89
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    Destabilizing effect of a fluorouracil extra base in a hybrid RNA duplex compared with bromo and chloro analogues (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1609-1613 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: In the presence of cobalt, rhodium or iridium hexammine salts, the RNA/DNA hybrid r-GCUUCGGC-dXU (with X = F, Cl or Br) crystallizes as a double-stranded helix with four consecutive G–U and C–U mismatches. The deoxy chloro- and bromouracil derivatives are isomorphous, space group C2, unit-cell parameters a = 53.80, b = 19.40, c = 50.31 Å, β = 109.9°, with the same infinite helix arrangement in the packing along the c axis with one extra DNA halogenouracil base included in the stacking. However, the fluorouracil derivative, with unit-cell parameters a = 53.75, b = 19.40, c = 45.84 Å, β = 105.7°, is not isomorphous. The corresponding extra DNA base dFU of the second strand is ejected out of the helical stack, leading to a shortening of the c axis. The specific destabilization of the fluorouracil for the duplex building is analyzed in terms of the polarization effect of the halogen atom attached to the 3′-terminal base that modulates its interactions.
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    URL: http://dx.doi.org/10.1107/S0907444901012318
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  • 90
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    Overexpression, purification, crystallization and preliminary X-ray diffraction analysis of Cu,Zn superoxide dismutase from Peking duck (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1646-1649 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The cDNA encoding Peking duck Cu,Zn superoxide dismutase (dSOD) was cloned and sequenced. The recombinant enzyme was overexpressed in Escherichia coli, purified to homogeneity and crystallized using the sitting-drop vapour-diffusion technique. Trigonal crystals of dSOD were obtained at 278 K at low ionic strength and around neutral pH. These crystals belong to space group P3221, with unit-cell parameters a = 124.4, c = 163.5 Å, γ = 120°. The asymmetric unit contains four dimers (eight monomers of Cu,Zn dSOD) and has a 56% solvent content, with a VM of 2.8 Å3 Da−1. On a Rigaku R-AXIS IIc image-plate area-detector system, the crystal diffracted to 2.9 Å. Unusual supermolecular double-helix packing with 922 non-crystallographic symmetry in crystals has been observed in the initial structural analysis.
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    URL: http://dx.doi.org/10.1107/S0907444901011106
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    Preliminary X-ray diffraction studies of the external functional unit RtH2-e from the Rapana thomasiana (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1663-1665 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The `external' oxygenated functional unit RtH2-e of the Rapana hemocyanin subunit RHSS2 was isolated and crystallized. X-ray intensity data to 3.3 Å resolution have been collected at 100 K and the structure has been solved using the molecular-replacement method. The space group is assigned to be the tetragonal P43212, with unit-cell parameters a = b = 105.5, c = 375.0 Å.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901012124
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    Crystallization and preliminary X-ray analysis of the archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1659-1662 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The archaeosine tRNA-guanine transglycosylase from the hyperthermophilic archaeon Pyrococcus horikoshii was crystallized and preliminary X-ray characterization was performed. Single crystals were grown by the hanging-drop vapour-diffusion method, using sodium/potassium phosphate and sodium acetate as precipitants. The space group is P41212 or P43212, with unit-cell parameters a = b = 99.28 (14), c = 363.74 (56) Å. The cryocooled crystals diffracted X-rays beyond 2.2 Å resolution using synchrotron radiation from station BL44XU at SPring-8 (Harima). Selenomethionine-substituted protein crystals were prepared in order to solve the structure by the MAD phasing method.
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    URL: http://dx.doi.org/10.1107/S0907444901011994
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    Purification, crystallization and preliminary X-ray diffraction studies of disintegrin (schistatin) from saw-scaled viper (Echis carinatus) (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1669-1670 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: This is the first report of crystallographic data on a disintegrin molecule from any source. The heterodimeric disintegrin with a molecular weight of 14 kDa from Echis carinatus venom is a potent antagonist of α4 integrins. The intact disintegrin, containing two subunits A and B, was isolated and purified using affinity and ion-exchange columns. It has been crystallized using 1.6 M ammonium sulfate as a precipitating agent. The crystals grew to dimensions of 0.25 × 0.20 × 0.20 mm and diffracted to 2.5 Å resolution. The crystals belong to space group I4122, with unit-cell parameters a = b = 91.7, c = 55.1 Å. Assuming a molecular weight of 14 kDa, a VM of 2.1 Å3 Da−1 is obtained for one molecule of disintegrin in the asymmetric unit.
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    URL: http://dx.doi.org/10.1107/S0907444901012082
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    Crystallization and X-ray diffraction measurements on recombinant molbindin, MopII, from Clostridium pasteurianum (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1715-1717 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Clostridium pasteurianum carries three genes termed mopI, II and III encoding three molbindin isoforms, one of which has been cloned, the gene product expressed in high yield and crystallized using the hanging-drop vapour-diffusion method. Well ordered monoclinic crystals in two different crystal forms, both with space group C2, were obtained in the presence and absence of Na2MoO4 and Na2WO4. Ligand-bound MopII crystallized with polyethylene glycol (PEG) 400 as a precipitant, whereas apo MopII required PEG 6000. High-resolution diffraction data were collected for ligand-bound MopII structures using synchrotron radiation to 1.8 and 1.6 Å resolution for the molybdate and tungstate complexes, respectively. Data were collected on apoMopII crystals to a resolution of 1.8 Å in-house.
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    URL: http://dx.doi.org/10.1107/S0907444901013798
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    Crystallization and preliminary X-ray diffraction analysis of glutathione-dependent dehydroascorbate reductase from spinach chloroplasts (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1726-1728 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Glutathione-dependent dehydroascorbate reductase (GSH-DHAR) catalyzes the reduction of dehydroascorbate to ascorbate using reduced glutathione as the electron donor. GSH-DHAR from spinach chloroplasts produced in Escherichia coli was crystallized by the hanging-drop vapour-diffusion method. The crystals were monoclinic, space group C2, with unit-cell parameters a = 98.25, b = 39.96, c = 106.86 Å, β = 110.46°. The asymmetric unit contained two molecules, giving a crystal volume per enzyme mass (VM) of 2.06 Å3 Da−1 and a solvent content of 40.3%. A full set of X-ray diffraction data were collected to 2.2 Å Bragg spacing from three native crystals with an overall Rmerge of 6.5% and a completeness of 93.4%.
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    The 1.6 Å resolution crystal structure of a mutant plastocyanin bearing a 21–25 engineered disulfide bridge (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1735-1738 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Plastocyanin is an electron-transfer protein which has been largely used for biophysical studies as well as for protein-engineering experiments. A surface disulfide bridge has been engineered in poplar plastocyanin to allow protein chemisorption on gold substrates. The mutated plastocyanin crystal structure has been studied at 1.6 Å resolution (R factor = 0.145, Rfree = 0.205) to characterize the effects of the engineered disulfide on the overall protein structure and on the Cu-coordination sphere in view of biophysical applications. The new orthorhombic crystal form isolated for the mutated plastocyanin displays two protein molecules per asymmetric unit.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901013221
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    Automated data processing on beamline FIP (BM30A) at ESRF (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1752-1753 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Automation of protein crystallography synchrotron beamlines is becoming necessary to face challenging structural genomics projects. In this context, a program has been developed that processes diffraction frames using popular software but analyzes statistics and makes choices the way crystallographers usually do. This program includes the classical peak search, indexing, integration, scaling and anomalous signal analysis. The result, comparable with that obtained by standard users, is rapidly available, providing the required information for a more efficient use of the beam time.
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    URL: http://dx.doi.org/10.1107/S0907444901013385
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    Multiple isomorphous replacement on merohedral twins: structure determination of deacetoxycephalosporin C synthase (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1776-1785 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Merohedral twinning is a packing anomaly that seriously impairs the determination of macromolecular crystal structures. Crystals of deacetoxycephalosporin C synthase (DAOCS), an enzyme involved in the expansion of the penicillin nucleus to form the core structure of the cephalosporin antibiotics, were found to be merohedrally twinned by many diagnostic criteria. Here, the structure determination of DAOCS from twinned crystals based on a combination of isomorphous replacement and the use of a multiple-wavelength diffraction data set is described.
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    URL: http://dx.doi.org/10.1107/S0907444901014081
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    Spherical plant viruses: interactions in solution, phase diagrams and crystallization of brome mosaic virus (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1799-1812 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Brome mosaic virus (BMV) is a small icosahedral plant virus of mean diameter 268 Å. Interactions between BMV particles in solution were studied by means of small-angle X-ray scattering in order to find crystallization conditions. The interactions between biomacromolecules as large as these viruses have not yet been systematically studied by this method. As it is known that usually proteins crystallize in, or close to, attractive regimes, the interactions between BMV particles in solution were studied as a function of pH, type of salt and size and concentration of polyethylene glycol. An unexpected result of these studies is that the precipitates obtained upon addition of PEG alone or PEG combined with salt were in fact made of microcrystals, which were all characterized by the same series of diffraction peaks, with positions close to those of a centered cubic space group. A phase diagram of the virus as a function of PEG concentration was established by means of microbatch experiments. From the precipitation zones, conditions for crystallization were tested from 5 to 40 mg ml−1 virus with 3−10%(w/v) PEG 8000 or PEG 20 000. Small crystals were obtained in several conditions after a few days and continued growing for several weeks.
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    URL: http://dx.doi.org/10.1107/S0907444901014949
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    Binding of N-acetylglucosamine to chicken egg lysozyme: a powder diffraction study (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1836-1842 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The binding of N-acetylglucosamine (NAG) to chicken egg lysozyme (E.C. 3.2.1.17) was investigated by high-resolution X-ray powder diffraction at room temperature. NAG was found to bind to lysozyme in a rapid precipitation preparation with 0.05 M NaCl buffer pH 6.0, but not 0.05 M NaCl buffer pH 5.0. Binding was indicated by significant and readily apparent changes in the diffraction pattern from that of the apo protein precipitated from the same solvent. The location of NAG bound to lysozyme was easily found from a difference Fourier map generated from structure factors extracted during a preliminary combined Rietveld and stereochemical restraint refinement. Full protein and protein–NAG structures were refined with these techniques (Rwp = 2.22–2.49%, Rp = 1.79–1.95%, R_F^2 = 4.95–6.35%) and revealed a binding mode for NAG which differed from that found in an earlier single-crystal study and probably represents a precursor trapped by rapid precipitation.
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    URL: http://dx.doi.org/10.1107/S0907444901015748
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