Source:http://linkedlifedata.com/resource/pubmed/id/21460452
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| Predicate | Object |
|---|---|
| rdf:type | |
| lifeskim:mentions | |
| pubmed:issue |
Pt 4
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| pubmed:dateCreated |
2011-4-4
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| pubmed:abstractText |
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 not 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.
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| pubmed:grant | |
| pubmed:commentsCorrections |
http://linkedlifedata.com/resource/pubmed/commentcorrection/21460452-10531526,
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http://linkedlifedata.com/resource/pubmed/commentcorrection/21460452-18156677,
http://linkedlifedata.com/resource/pubmed/commentcorrection/21460452-18600222,
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http://linkedlifedata.com/resource/pubmed/commentcorrection/21460452-8539602
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| pubmed:language |
eng
|
| pubmed:journal | |
| pubmed:citationSubset |
IM
|
| pubmed:chemical | |
| pubmed:status |
MEDLINE
|
| pubmed:month |
Apr
|
| pubmed:issn |
1399-0047
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| pubmed:author | |
| pubmed:issnType |
Electronic
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| pubmed:volume |
67
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| pubmed:owner |
NLM
|
| pubmed:authorsComplete |
Y
|
| pubmed:pagination |
338-44
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| pubmed:dateRevised |
2011-7-28
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| pubmed:meshHeading | |
| pubmed:year |
2011
|
| pubmed:articleTitle |
Using SAD data in Phaser.
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| pubmed:affiliation |
CIMR Haematology, University of Cambridge, Wellcome Trust/MRC Building, Cambridge, England. rjr27@cam.ac.uk
|
| pubmed:publicationType |
Journal Article,
Research Support, Non-U.S. Gov't,
Research Support, N.I.H., Extramural
|