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  • 1990-1994  (15)
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Material
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Year
  • 1
    Electronic Resource
    Electronic Resource
    On the application of phase relationships to complex structures. XXXIII. The problems with large structures and low resolution (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 13-17 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A conventional direct method, using the Sayre equation as a basis, has been shown to be capable of solving a small protein with data of 3.0 Å resolution or better. An analysis of the Sayre equation, with data of various resolutions and with different lower limits of |E| for the contributors in the summation, shows that its effectiveness for phasing is independent of structural complexity but does decline as the resolution becomes worse. It is suggested that a practicable lower limit for the application of conventional direct methods is about 3.5 Å. For large macromolecular structures the number of contributors to the summation in the Sayre equation becomes too large to handle and it is suggested that real-space methods should be used instead.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444992009624
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Direct-space methods in phase extension and phase determination. II. Developments of low-density elimination (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 367-371 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The low-density elimination method for phase extension and refinement [Shiono & Woolfson (1992). Acta Cryst. A48, 451–456] has been improved by substituting a smoother density-modification procedure for the original sharp cut-off function. In addition, better criteria have been found for limiting the number of refinement cycles, which gives a better final result for much less work. The effectiveness of the process has been illustrated by phase refinement for a protein with high-resolution (1.17 Å) data containing 808 independent non-H atoms plus 83 water molecules in the asymmetric unit; the unweighted mean-phase error was reduced from 74 to 39.3°. Phase extension and refinement was also demonstrated for pig 2Zn insulin starting with multiple isomorphous replacement (MIR) phases at 1.9 Å and extending out to 1.5 Å. There was a significant improvement of phases and the final map had a correlation coefficient of 0.540.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444993003282
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    The application of one-wavelength anomalous scattering. I. Combining results of different methods (1990)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 46 (1990), S. 656-659 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Two different techniques for employing one-wavelength anomalous scattering, one using a direct-methods approach and the other a Patterson-like function, are applied to two known protein structures. The first of these, avian pancreatic polypeptide, is in space group C2 with one molecule containing 36 amino-acid residues in the asymmetric unit. The second, ribonuclease Sa in space group P212121, has two molecules each containing 96 amino-acid residues in the asymmetric unit. Both methods give phase indications easily leading to the elucidation of the smaller structure and probably enabling the larger structure to be solved as well. For each structure the electron density maps from the phases given by the two methods are combined through a minimum function. The Fourier transform of the resultant map gives phases better than those given by the individual methods, reducing the mean phase error by 2-3°, which could be critical in some applications.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S010876739000352X
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    Paper (German National Licenses)
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  • 4
    Electronic Resource
    Electronic Resource
    The application of one-wavelength anomalous scattering. II. An analytical approach for phase determination (1990)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 46 (1990), S. 659-664 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: An analytical method has been developed by which phase estimates may be uniquely determined from one-wavelength anomalous-scattering data; the method as described can be applied to structures containing one type of anomalous scatterer. The method has been tested on two structures. The first is an Hg derivative of a small protein, avian pancreatic polypeptide (App), crystallizing in space group C2 with one molecule of 36 amino-acid residues in the asymmetric unit. The second is a Pt derivative of ribonuclease Sa (RNA), crystallizing in space group P212121 with two molecules of 96 amino-acid residues in the asymmetric unit. The phases for App give an electron density map which can easily be interpreted in terms of a model. For RNA the map is less clear but has strong similarities with the true map and could probably be interpreted. If anomalous scatterers are centrosymmetrically arranged then the analysis shows that there is a simple alternative process for calculating a map, called a Bp map, which directly shows a structural image.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0108767390003531
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    Paper (German National Licenses)
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  • 5
    Electronic Resource
    Electronic Resource
    Henry Lipson, 1910-1991 (1991)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 47 (1991), S. 635-636 
    Details
    ISSN: 1600-5724
    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/S0108767391006682
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    Paper (German National Licenses)
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  • 6
    Electronic Resource
    Electronic Resource
    On the application of phase relationships to complex structures. XXXII. A small protein at low resolution (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 9-12 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The direct-methods program SA YTAN is applied to data at various restricted resolutions for a small protein. It is shown that useful sets of phases can be obtained even down to 3 Å resolution. Conventional figures of merit are not very discriminating for the phase sets developed, but modified figures of merit seem capable of selecting the better phase sets, at least for those generated from 2 Å or higher resolution data.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444992009636
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    Paper (German National Licenses)
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  • 7
    Electronic Resource
    Electronic Resource
    On the application of one-wavelength anomalous scattering. IV. The absolute configuration of the anomalous scatterers (1994)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 50 (1994), S. 7-10 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: An essential first step in most techniques for using anomalous-scattering data for phase determination is to determine the positions of the anomalous scatterers. This is usually done by use of the anomalous differences, either as input to a direct-methods procedure or to produce a Patterson map. If the arrangement of anomalous scatterers is noncentrosymmetric then it is also necessary to find their absolute configuration and a process is described for doing this based on the properties of the Ps function [Okaya, Saito & Pepinsky (1955). Phys. Rev. 98, 1857–1858]. If the arrangement of anomalous scatterers is centrosymmetric then the problem does not occur.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444993008091
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  • 8
    Electronic Resource
    Electronic Resource
    Mean phase error and the map-correlation coefficient (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 530-533 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: In judging the effectiveness of methods of solving crystal structures, or in phase refinement and development, two criteria are commonly used. The first is the mean phase error, which may be weighted in some way, and the second is the map correlation coefficient which describes the similarity of a map with estimated phases to that with true phases. It is shown that these two measures are directly related and that given the individual phase errors the map correlation coefficient may be found without the need to calculate a map. Various aspects of this connection are examined, including the map correlation coefficient when weights are used for calculating maps and the conditions under which phase extension leads to maps with a higher map correlation coefficient – which involves a balance between the advantage of employing more data and the disadvantage that the extra data may have a higher average phase error.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444993005852
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  • 9
    Electronic Resource
    Electronic Resource
    On the application of phase relationships to complex structures. XXIX. Choosing the large Es (1991)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 47 (1991), S. 278-281 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The set of large Es through which a structure is solved by direct methods is usually chosen by a convergence or convergence–divergence process. This process aims to give a strong phase-extension pathway starting from a small set of Es whose phases are known or allocated in some way. Sometimes sets of reflexions thus obtained are poorly conditioned and under tangent-formula refinement even initially correct phases will degenerate to randomness. A simple new algorithm has been developed which improves the conditioning of the complete set of reflexions and their relationships and is more appropriate to current trends to start refinement from a complete set of random phases. A particular feature of this algorithm is that it maximizes the minimum number of relationships for any reflexion.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0108767391000958
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    Paper (German National Licenses)
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  • 10
    Electronic Resource
    Electronic Resource
    On the application of one-wavelength anomalous scattering. III. The Wilson-distribution and MPS methods (1991)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 47 (1991), S. 533-537 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: This paper describes two methods which break the ambiguity associated with phase determination from one-wavelength anomalous-scattering data when the positions of the anomalous scatterers are known. In the Wilson-distribution method the magnitudes of the contributions of the light atoms are found for each of the alternative phases and the phases are then given weights according to the usual Wilson probability distribution for the magnitudes. In the MPS method the two possible magnitudes of the contributions of the light atoms to the scattering are compared with a theoretical value based on the observed structure magnitudes and the Fourier coefficient of the |Ps| function [Hao & Wooifson (1989). Acta Cryst. A45, 794–797]. Once again this leads to a weight for each alternative phase. A best-estimate phase based on the two weights is compared with true phases for two known proteins consisting of 36 and 96 amino acid residues respectively. It is concluded that the quality of the phase estimates is similar to that obtained by other previously published procedures and that the results are much more limited by the magnitude of the anomalous contribution and the data quality than by the actual method used. The methods were then applied to the smaller protein structure using calculated data both with and without added errors. It is concluded that this common procedure for the testing of methods must be done with great care, otherwise unduly optimistic conclusions may be drawn.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0108767391003781
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