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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
    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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  • 5
    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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