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  • 1
    Electronic Resource
    Electronic Resource
    Use of Single Isomorphous Replacement Data of Proteins – Resolving the Phase Ambiguity and a New Procedure for Phase Extension (1997)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 53 (1997), S. 49-55 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A procedure combining direct methods and solvent flattening to break the phase ambiguity intrinsic to the single isomorphous replacement (SIR) technique has been tested with the experimental SIR data of the known protein RNase Sa at 2.5 Å resolution. The use of direct methods provided better initial phases for the solvent-flattening procedure, while the solvent-flattening procedure greatly improved direct-method phases leading to a traceable Fourier map. A small subset of known phases at low resolution makes direct phasing of SIR data much easier. Accordingly a method for extending low-resolution phases to high-resolution ones is proposed making use of additional SIR information. This reduces the problem of finding a value in the range of 0–2π for each unknown phase to that of just making a choice between two possible values. Tests with the known protein RNase Sa showed that the method is able to extend phases from a resolution of 6 to 2.5 Å leading to an easily traceable Fourier map. The solvent-flattening technique and the combination of which with direct methods were used for the phase extension. Either procedure yielded reasonably good results, but on the whole, the result from the combination of direct methods with solvent flattening is better. Results of the latter procedure were further compared with that from direct phasing of the 2.5 Å SIR data and with that from phase extension by solvent flattening without SIR information. An improvement gained by the use of SIR information is evident.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444996009365
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  • 2
    Electronic Resource
    Electronic Resource
    Direct-Space Methods in Phase Extension and Phase Refinement. V. The Histogram Moments Method (1996)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 1114-1118 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Any distribution is completely defined by its moments. It is shown that a process of phase refinement can be carried out, based on Fourier transforms, which modifies the moments of electron density, separately in the protein and solvent regions, towards target values. Tests have been carried out on two moderate-sized proteins with 800–900 atoms in the asymmetric unit, one containing heavy atoms and the other not. It has been found that refinement using the third moment about zero in the protein region is most effective and that refinement with higher moments, or in the solvent region, adds nothing useful. Two kinds of weights are necessary in the method. One is for giving a weighted mixture of new phase indications with original phase estimates from, say, multiple isomorphous replacement. The other weights are applied to the Fourier coefficients of density maps to give the best possible signal:noise ratio. These weights have been explored empirically and the best ones found are described. It is concluded that since the moments method, which changes phases in reciprocal space, is independent of other histogram-matching procedures, which change density in real space, it has something to offer in a refinement package containing several procedures.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444996008451
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  • 3
    Electronic Resource
    Electronic Resource
    A new iterative procedure for combining direct methods with solvent flattening – dealing with the phase ambiguity in protein crystallography (1997)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 53 (1997), S. 792-794 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A new procedure for combining direct methods with the solvent-flattening technique is proposed for phasing single isomorphous replacement (SIR) or one-wavelength anomalous scattering (OAS) data of proteins. The new procedure differs from the previous one [Zheng, Zheng, Gu, Mo, Fan & Hao (1997). Acta Cryst. D53, 49–55] in that the direct method not only provides input phases to but also accepts feedback phases from solvent flattening, thus forming an iterative process for breaking the ambiguities and refining the values of phases. The new procedure was tested with the experimental SIR data of the known structure ribonuclease Sa. For the strongest 1000 of the total 7264 refelctions, the mean Fobs-weighted phase error is 7.5 and 9.4° lower than that of the previous procedure and that of solvent flattening alone, respectively.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S090744499700680X
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  • 4
    Electronic Resource
    Electronic Resource
    The program SAPI and its applications. III. Determination of structures having pseudo-translational symmetry (1990)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 46 (1990), S. 99-103 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Optimization has been made of the program SAPI for automatic solution of structures having pseudo-translational symmetry. This includes: (1) floating default cutoff of E's; (2) automatic and user-adjustable balance between the number of systematically strong reflections and that of the systematically weak ones; (3) R factors for reflection subsets corresponding to the 'strong' group and the 'weak' groups. Examples on solving structures with pseudo-translational symmetry are discussed in detail. They include known as well as unknown structures and centrosymmetric as well as non-centrosymmetric structures, all of which can be solved starting from a default run of SAPI.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0108767389010147
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  • 5
    Electronic Resource
    Electronic Resource
    Direct-method-aided phasing of MAD data (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 250-253 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The direct methods of breaking the phase ambiguity intrinsic in one-wavelength anomalous scattering (OAS) data and MAD phasing are powerful methods in their own rights. In a different context, in addition to their success in phasing OAS data, direct methods can also be useful in the treatment of MAD data. The idea has been tested with the MAD data at 2.5 Å resolution from the protein human adenosine kinase [Mathews et al. (1998), Biochemistry, 37, 15607–15620]. The results showed that the incorporation of direct methods in MAD phasing led to a significant improvement of phases over those obtained from the conventional MAD phasing method alone, as indicated by improved map correlation coefficients (with the existing model), reduced phase errors by 4.5° and improved map connectivity.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900018606
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  • 6
    Electronic Resource
    Electronic Resource
    Crystallization and preliminary X-ray diffraction studies of recombinant staphylokinase (1996)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 564-565 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Staphylokinase, a fibrin-specific plasminogen activator, was highly expressed in Escherichia coli and purified by ion-exchange and gel-filtration chromatography. The purified recombinant staphylokinase was fully active and readily crystallized against 1.2 M sodium citrate in 100 mM Tris–HCl buffer at pH 8.0 using the hanging-drop method. Crystals of staphylokinase diffract to better than 2.2 Å resolution. The crystal belongs to the tetragonal space group P41212 or its enantiomorph with unit-cell parameters a = b = 67.5, c = 150.1 Å. There are two molecules in the asymmetric unit. In this paper, we described the first crystallization of a kind of plasminogen activator and present the results of preliminary X-ray diffraction data from the native protein.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444995013552
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  • 7
    Electronic Resource
    Electronic Resource
    Solving crystal structures from two-wavelength X-ray powder diffraction data – breaking the phase ambiguity in the noncentrosymmetric case (2000)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 592-595 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Direct methods of breaking phase ambiguities in protein crystallography have been introduced in powder diffraction analysis. This is aiming at ab initio solution of noncentrosymmetric structures using two-wavelength anomalous powder diffraction data. The known structure of the hydrogen bromide salt of leotidine (C14H20O2N2·HBr) in space group P212121 was used for simulating two-wavelength anomalous powder diffraction with the Br atom as anomalous scatterer. X-ray wavelengths are selected at \lambda_1 = 0.920 and \lambda_2 = 1.500 Å. Unique reflections from the diffraction pattern of \lambda_2 were able to locate the Br atom accurately. All overlapping diffraction peaks were uniformly partitioned to decompose into single reflections. Structure-factor amplitudes were then extracted. With these and the substructure of Br atoms, unique phases for centric reflections (hk0, h0l and 0kl) and phase doublets for noncentric reflections were obtained. The direct method was used to break the phase ambiguity leading to an interpretable electron-density map, from which five cycles of Fourier iteration yielded the complete structure.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0108767300011417
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  • 8
    Electronic Resource
    Electronic Resource
    OASIS: a computer program for breaking phase ambiguity in one-wavelength anomalous scattering or single isomorphous substitution (replacement) data (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 980-981 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The phase problem is reduced to a sign problem once the anomalous-scatterer or the replacing-heavy-atom sites are located. OASIS adopts the CCP4 format [Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760–763]. It applies a direct-method procedure to break the phase ambiguity intrinsic to one-wavelength anomalous scattering (OAS) or single isomorphous replacement (SIR) data.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889800001424
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  • 9
    Electronic Resource
    Electronic Resource
    A Method of Electron Diffraction Intensity Correction in Combination with High-Resolution Electron Microscopy (1996)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 152-157 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: An empirical method is proposed for partially correcting the distortion of electron diffraction intensity caused by Ewald-sphere curvature, crystal bending, thickness inhomogeneity etc. The method is based on the combination of electron diffraction and high-resolution electron microscopy. It has been tested with a crystal of high-temperature superconducting oxide YBa2Cu3O7−x and shown to be effective.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0108767395012682
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  • 10
    Electronic Resource
    Electronic Resource
    Structure of guanidinium pentamolybdobis(n-propylarsenate) dihydrate (1988)
    Oxford [u.a.] : International Union of Crystallography (IUCr)
    Acta crystallographica 44 (1988), S. 1503-1505 
    Details
    ISSN: 1600-5759
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0108270188004512
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