2q4w: Difference between revisions

Revision as of 12:35, 10 July 2008

This article has been automatically seeded. Changes to this page should pertain to the PDB entry only and not to the protein or biomolecule in general.

File:2q4w.png

Template:STRUCTURE 2q4w

Ensemble refinement of the protein crystal structure of cytokinin oxidase/dehydrogenase (CKX) from Arabidopsis thaliana At5g21482Ensemble refinement of the protein crystal structure of cytokinin oxidase/dehydrogenase (CKX) from Arabidopsis thaliana At5g21482

Template:ABSTRACT PUBMED 17850744

About this StructureAbout this Structure

2Q4W is a Single protein structure of sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA.

ReferenceReference

Ensemble refinement of protein crystal structures: validation and application., Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr, Structure. 2007 Sep;15(9):1040-52. PMID:17850744

Page seeded by OCA on Thu Jul 10 12:35:57 2008

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-'''Ensemble refinement of the protein crystal structure of cytokinin oxidase/dehydrogenase (CKX) from Arabidopsis thaliana At5g21482'''
+===Ensemble refinement of the protein crystal structure of cytokinin oxidase/dehydrogenase (CKX) from Arabidopsis thaliana At5g21482===
-==Overview==
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-X-ray crystallography typically uses a single set of coordinates and B factors to describe macromolecular conformations. Refinement of multiple copies of the entire structure has been previously used in specific cases as an alternative means of representing structural flexibility. Here, we systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of the distributions of atomic positions in the simulated structures than single-conformer refinements. Comparison of principal components calculated from the refined ensembles and simulations shows that concerted motions are captured locally, but that correlations dissipate over long distances. Ensemble refinement is also used on 50 experimental structures of varying resolution and leads to decreases in R(free) values, implying that improvements in the representation of flexibility observed for the simulated structures may apply to real structures. These gains are essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from ensemble refinement.
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 [[Category: Refinement methodology development]]
 [[Category: Structural genomic]]
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