期刊
STRUCTURE
卷 15, 期 9, 页码 1040-1052出版社
CELL PRESS
DOI: 10.1016/j.str.2007.06.019
关键词
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资金
- NIGMS NIH HHS [U54 GM074901, T32 GM007215-26, T32 GM007215, U54 GM074901-01, GM 07215, U54 GM 0749011] Funding Source: Medline
- NLM NIH HHS [T15 LM007359, T15 LM 007359, T15 LM007359-05] Funding Source: Medline
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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