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2q4d

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{{STRUCTURE_2q4d| PDB=2q4d | SCENE= }}
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'''Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from Arabidopsis thaliana gene At5g11950'''
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===Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from Arabidopsis thaliana gene At5g11950===
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==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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(as it appears on PubMed at http://www.pubmed.gov), where 17850744 is the PubMed ID number.
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{{ABSTRACT_PUBMED_17850744}}
==About this Structure==
==About this Structure==
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[[Category: Structural genomic]]
[[Category: Structural genomic]]
[[Category: Unknown function]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 14:19:12 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 10 12:37:12 2008''

Revision as of 09:37, 10 July 2008

Image:2q4d.png

Template:STRUCTURE 2q4d

Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from Arabidopsis thaliana gene At5g11950

Template:ABSTRACT PUBMED 17850744

About this Structure

2Q4D is a Single protein structure of sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA.

Reference

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 12:37:12 2008

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