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  • 1
    Electronic Resource
    Electronic Resource
    Phasing with mercury at 1 Å wavelength (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 814-818 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Synchrotron sources provide a continuously tunable X-ray beam which makes it possible to optimize the anomalous contribution to phase determination using heavy-atom replacement. This method was used to solve two protein structures, those of Dictyostelium discoideum nucleoside diphosphate kinase and of lobster enolase. The first had 17 kDa of protein in the asymmetric unit, the second, 47 kDa. In both cases, a single mercury derivative yielded single isomorphous replacement with anomalous-scattering phases from which an interpretable electron-density map was derived by solvent flattening. The efficient solution of the X-ray structure was largely due to the large anomalous scattering of mercury at a wavelength shorter than the LIII absorption edge.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444995000655
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  • 2
    Electronic Resource
    Electronic Resource
    Crystallization of the dimerization-initiation site of genomic HIV-1 RNA: preliminary crystallographic results (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 281-284 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The genomic RNA of all retroviruses is encapsidated in virions as a dimer of single-stranded chains held together near their 5′-end. For HIV-1, the initial site of dimerization has been shown to be a hairpin with a nine-residue loop containing a self-complementary sequence of six residues. This structure is proposed to promote dimerization by loop–loop interaction and formation of a so-called `kissing complex'. A 23-nucleotide RNA strand containing the loop enclosed by a seven base-pair stem has been synthesized. This oligomer was crystallized by the vapour-diffusion method at 310 K, pH 6.5, with methyl-pentanediol as the precipitant agent in the presence of MgCl2, KCl and spermine. Quasi-complete diffraction data were obtained at 2.7 Å resolution with a conventional X-ray source and at 2.3 Å resolution on a synchrotron beamline. The space group is P3121 or its enantiomorph P3221, with cell parameters a = b = 60.1, c = 65.9 Å at ambient temperature, or a = b = 59.0, c = 64.3 Å in a nitrogen-gas stream. There are two oligomers per asymmetric unit as determined from absorbance measurements of a dissolved crystal whose volume was carefully determined. In some cases, either perfectly or partially twinned crystals were obtained. Perfect twinning is detected by an apparent hexagonal symmetry and yields unusable crystallographic data, whilst partial twinning yields usable data after adequate processing. Structure solution is under way by searching for heavy-atom derivatives and systematically substituting bromo- or iodo-uridines for uridines.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444998008506
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  • 3
    Electronic Resource
    Electronic Resource
    MAD on threonine synthase: the phasing power of oxidized selenomethionine (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1337-1340 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The use of selenomethionine and anomalous dispersion has become the most widely used way of solving the phase problem for de novo protein structure determination. In this paper, MAD data collected from oxidized and reduced selenomethionine-containing protein are described, and it is shown that oxidized selenomethionine has a very strong phasing power and can be efficiently used if the oxidation is uniform. The comparison was performed on threonine synthase crystals. For example, the phasing power of the oxidized data is doubled for the dispersive signal and is 20% stronger for the anomalous signal at the peak wavelength. The strength of the anomalous signal can be used to improve the signal when a protein contains few methionines or for single anomalous dispersion. The oxidation of some selenomethionines shows in the electron-density map through the presence of water molecules within hydrogen-bonding distance of the putative O atom.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901008666
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  • 4
    Electronic Resource
    Electronic Resource
    Expression, purification, crystallization and preliminary X-ray analysis of the cathelicidin motif of the protegrin-3 precursor (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1677-1679 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Numerous precursors of antibacterial peptides with unrelated sequences share a similar prosequence which belongs to the cathelicidin family of proteins. The three-dimensional structure of this cathelicidin motif, which contains two disulfide bonds, has not yet been reported. The cathelicidin motif (ProS) of the protegrin-3 precursor was overexpressed in Escherichia coli as a His-tagged protein. The His6 tag was removed by thrombin cleavage. ProS was purified to homogeneity and single crystals were obtained by the hanging-drop vapour-diffusion method at pH 3–4. Preliminary X-ray diffraction analysis indicated that these crystals belong to the hexagonal space group P6122 or P6522, with unit-cell parameters a = b = 51.42, c = 134.25 Å. These crystals diffracted beyond 2.75 Å (1.9 Å at ESRF) and contain one molecule per asymmetric unit.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901012598
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  • 5
    Electronic Resource
    Electronic Resource
    Structure of spinach acetohydroxyacid isomeroreductase complexed with its reaction product dihydroxymethylvalerate, manganese and (phospho)-ADP-ribose (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 389-397 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Acetohydroxyacid isomeroreductase catalyses a two-step reaction composed of an alkyl migration followed by an NADPH-dependent reduction. Both steps require a divalent cation and the first step has a strong preference for magnesium. Manganese ions are highly unfavourable to the reaction: only 3% residual activity is observed in the presence of this cation. Acetohydroxyacid isomeroreductase has been crystallized with its substrate, 2-aceto-2-hydroxybutyrate (AHB), Mn2+ and NADPH. The 1.6 Å resolution electron-density map showed the reaction product (2,3-dihydroxy-3-methylvalerate, DHMV) and a density corresponding to (phospho)-ADP-ribose instead of the whole NADP+. This is one of the few structures of an enzyme complexed with its reaction product. The structure of this complex was refined to an R factor of 19.3% and an Rfree of 22.5%. The overall structure of the enzyme is very similar to that of the complex with the reaction-intermediate analogue IpOHA [N-hydroxy-N-isopropyloxamate; Biou et al. (1997), EMBO J. 16, 3405–3415]. However, the active site shows some differences: the nicotinamide is cleaved and the surrounding amino acids have rearranged accordingly. Comparison between the structures corresponding to the reaction intermediate and to the end of the reaction allowed the proposal of a reaction scheme. Taking this result into account, the enzyme was crystallized with Ni2+ and Zn2+, for which only 0.02% residual activity were measured; however, the crystals of AHB/Zn/NADPH and of AHB/Ni/NADPH also contain the reaction product. Moreover, mass-spectrometry measurements confirmed the cleavage of nicotinamide.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900001694
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  • 6
    Electronic Resource
    Electronic Resource
    An efficient method for solving RNA structures: MAD phasing by replacing magnesium with zinc (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 330-332 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of a 46-nucleotide RNA complex has been successfully solved using multi-wavelength anomalous dispersion (MAD) at the zinc K edge. Taking advantage of the eight magnesium-binding sites, it has been shown that for five of them magnesium could be replaced by zinc. This resulted in an excellent 2.0 Å MAD electron-density map. Zinc, in common with some other transition metals, is able to replace magnesium in RNA structures, but zinc has the advantage of its K edge being ideally located at 1.284 Å. As most RNA molecules contain magnesium-binding sites, it is suggested that this method could be a valuable alternative to the use of bromo derivatives of bases, which is limited to chemically synthesizable and thus rather short RNA sequences.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900017558
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  • 7
    Electronic Resource
    Electronic Resource
    Detection and treatment of twinning: an improvement and new results (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1179-1187 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: This work deals with two aspects of the twinning problem. Firstly, an improvement of a known statistical test aimed at detecting twinning is presented and, secondly, a new parametrization of twinning is described, as well as a new method to obtain an accurate estimate of the degreee of twinning. During work on crystals of the dimerization-initiation site of the HIV-1 genomic RNA, perfectly twinned crystals were obtained which were not immediately recognized as such by use of a known statistical method. This method, reminiscent of Wilson tests for the detection of centrosymmetric space groups, relies on the calculation of 〈F^{2}〉/〈F〉2 or, equivalently, of 〈I2〉/〈I〉2. It is shown that overlooking experimental errors may lead to erroneously large values of this index and, in turn, to ambiguous or incorrect conclusions. An immediate solution to this problem is presented. Independently, an alternative parametrization which expresses both the effect of twinning on intensities and the operation of untwinning to recover the correct intensities is proposed. A new method for estimating the degree of twinning is also presented. It is based upon maximization of the cross-correlation coefficients between intensities of all available data sets, and yields a fully analytical solution. Tests made with experimental data are quite satisfactory. It is suggested that the latter results could be used efficiently within the MIR method by allowing refinement, through one additional parameter only, of the twinning ratios of all data sets considered for phasing. Finally, the new parametrization of twinning has striking consequences in this correlation-based twinning determination: very unexpectedly, it yields a novel estimate of the `twinning ratio' of a potentially twinned crystal which is fully independent of the data set used for the comparison.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444999004758
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  • 8
    Electronic Resource
    Electronic Resource
    Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals (1988)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 44 (1988), S. 112-124 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Four transfer RNA crystals, the monoclinic and orthorhombic forms of yeast tRNAPhe as well as forms A and B of yeast tRNAAsp, have been submitted to the same restrained least-squares refinement program and refined to an R factor well below 20% for about 4500 reflections between 10 and 3 Å. In yeast tRNAAsp crystals the molecules exist as dimers with base pairings of the anticodon (AC) triplets and labilization of the tertiary interaction between one invariant guanine of the dihydrouridine (D) loop and the invariant cytosine of the thymine (T) loop (G 19-C56). In yeast tRNAPhe crystals, the molecules exist as monomers with only weak intermolecular packing contacts between symmetry-related molecules. Despite this, the tertiary folds of the L-shaped tRNA structures are identical when allowance is made for base sequence changes between tRNAPhe and tRNAAsp. However, the relative mobilities of two regions are inverse in the two structures with the AC loop more mobile than the D loop in tRNAPhe and the D loop more mobile than the AC loop in tRNAAsp. In addition, the T loop becomes mobile in tRNAAsp. The present refinements were performed to exclude packing effects or refinement bias as possible sources of such differential dynamic behavior. It is concluded that the transfer of flexibility from the anticodon to the D- and T-loop region in tRNAAsp is not a crystalline artefact. Further, analysis of the four structures supports a mechanism for the flexibility transfer through base stacking in the AC loop and concomitant variations in twist angles between base pairs of the anticodon helix which propagate up to the D- and T-loop region.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S010876738700446X
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  • 9
    Electronic Resource
    Electronic Resource
    Measurement of the atomic coordinates of a Kendrew-type model from two projections (1983)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 16 (1983), S. 658-659 
    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/S0021889883011310
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  • 10
    Electronic Resource
    Electronic Resource
    A real-time interactive graphics program to determine crystal orientation for the analysis of oscillation diffraction photographs (1986)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 19 (1986), S. 28-33 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: This paper describes a powerful preliminary to various least-squares programs for finding the exact crystal orientation for the oscillation method. It is well suited to cases of large initial misorientation. It uses the real-time rotation and clipping capabilities of the high-performance graphics system PS300 from Evans & Sutherland. A program has been written that performs a geometrical inversion of reciprocal space through its origin and manipulates this transformed image in place of the direct one. The Ewald sphere is thus transformed into a plane that can be superimposed on the film. The crossing of any reciprocal-lattice point through the Ewald sphere is then replaced by the crossing of its transform through the film plane. Clipping allows elimination of all the points too far away from this plane, i.e. those that are not in a diffraction condition. Determination of the correct orientation is achieved by superimposing the inverted reciprocal-lattice image on the corresponding transformed image of the observed film.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889886090040
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