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Title: Phaser crystallographic software

Abstract

No abstract prepared.

Authors:
; ; ; ; ;
Publication Date:
Research Org.:
COLLABORATION - University of Cambridge,UK
OSTI Identifier:
932570
Report Number(s):
LBNL-63582
Journal ID: ISSN 0021-8898; JACGAR; R&D Project: 863C1F; TRN: US200813%%43
DOE Contract Number:
DE-AC02-05CH11231
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Applied Crystallography; Journal Volume: 40; Related Information: Journal Publication Date: August 2007
Country of Publication:
United States
Language:
English
Subject:
99; CRYSTALLOGRAPHY; P CODES; MOLECULES; PHASE STUDIES

Citation Formats

McCoy, Airlie J., Grosse-Kunstleve, Ralf W., Adams, Paul D., Winn, Martin D., Storoni, Laurent C., and Read, Randy J. Phaser crystallographic software. United States: N. p., 2007. Web. doi:10.1107/S0021889807021206.
McCoy, Airlie J., Grosse-Kunstleve, Ralf W., Adams, Paul D., Winn, Martin D., Storoni, Laurent C., & Read, Randy J. Phaser crystallographic software. United States. doi:10.1107/S0021889807021206.
McCoy, Airlie J., Grosse-Kunstleve, Ralf W., Adams, Paul D., Winn, Martin D., Storoni, Laurent C., and Read, Randy J. Mon . "Phaser crystallographic software". United States. doi:10.1107/S0021889807021206.
@article{osti_932570,
title = {Phaser crystallographic software},
author = {McCoy, Airlie J. and Grosse-Kunstleve, Ralf W. and Adams, Paul D. and Winn, Martin D. and Storoni, Laurent C. and Read, Randy J.},
abstractNote = {No abstract prepared.},
doi = {10.1107/S0021889807021206},
journal = {Journal of Applied Crystallography},
number = ,
volume = 40,
place = {United States},
year = {Mon Mar 26 00:00:00 EDT 2007},
month = {Mon Mar 26 00:00:00 EDT 2007}
}
  • Protein fragments suitable for use in molecular replacement can be generated by normal-mode perturbation, analysis of the difference distance matrix of the original versus normal-mode perturbed structures, and SCEDS, a score that measures the sphericity, continuity, equality and density of the resulting fragments. A method is described for generating protein fragments suitable for use as molecular-replacement (MR) template models. The template model for a protein suspected to undergo a conformational change is perturbed along combinations of low-frequency normal modes of the elastic network model. The unperturbed structure is then compared with each perturbed structure in turn and the structurally invariantmore » regions are identified by analysing the difference distance matrix. These fragments are scored with SCEDS, which is a combined measure of the sphericity of the fragments, the continuity of the fragments with respect to the polypeptide chain, the equality in number of atoms in the fragments and the density of C{sup α} atoms in the triaxial ellipsoid of the fragment extents. The fragment divisions with the highest SCEDS are then used as separate template models for MR. Test cases show that where the protein contains fragments that undergo a change in juxtaposition between template model and target, SCEDS can identify fragments that lead to a lower R factor after ten cycles of all-atom refinement with REFMAC5 than the original template structure. The method has been implemented in the software Phaser.« less
  • SAD data can be used in Phaser to solve novel structures, supplement molecular-replacement phase information or identify anomalous scatterers from a final refined model. Phaser is a program that implements likelihood-based methods to solve macromolecular crystal structures, currently by molecular replacement or single-wavelength anomalous diffraction (SAD). SAD phasing is based on a likelihood target derived from the joint probability distribution of observed and calculated pairs of Friedel-related structure factors. This target combines information from the total structure factor (primarily non-anomalous scattering) and the difference between the Friedel mates (anomalous scattering). Phasing starts from a substructure, which is usually but notmore » necessarily a set of anomalous scatterers. The substructure can also be a protein model, such as one obtained by molecular replacement. Additional atoms are found using a log-likelihood gradient map, which shows the sites where the addition of scattering from a particular atom type would improve the likelihood score. An automated completion algorithm adds new sites, choosing optionally among different atom types, adds anisotropic B-factor parameters if appropriate and deletes atoms that refine to low occupancy. Log-likelihood gradient maps can also identify which atoms in a refined protein structure are anomalous scatterers, such as metal or halide ions. These maps are more sensitive than conventional model-phased anomalous difference Fouriers and the iterative completion algorithm is able to find a significantly larger number of convincing sites.« less
  • Four case studies in using maximum-likelihood molecular replacement, as implemented in the program Phaser, to solve structures of protein complexes are described. Molecular replacement (MR) generally becomes more difficult as the number of components in the asymmetric unit requiring separate MR models (i.e. the dimensionality of the search) increases. When the proportion of the total scattering contributed by each search component is small, the signal in the search for each component in isolation is weak or non-existent. Maximum-likelihood MR functions enable complex asymmetric units to be built up from individual components with a ‘tree search with pruning’ approach. This method,more » as implemented in the automated search procedure of the program Phaser, has been very successful in solving many previously intractable MR problems. However, there are a number of cases in which the automated search procedure of Phaser is suboptimal or encounters difficulties. These include cases where there are a large number of copies of the same component in the asymmetric unit or where the components of the asymmetric unit have greatly varying B factors. Two case studies are presented to illustrate how Phaser can be used to best advantage in the standard ‘automated MR’ mode and two case studies are used to show how to modify the automated search strategy for problematic cases.« less
  • No abstract prepared.
  • No abstract prepared.