Ensemble refinement of protein crystal structures: validation and application.Levin, E.J., Kondrashov, D.A., Wesenberg, G.E., Phillips, G.N.
(2007) Structure 15: 1040-1052
- PubMed: 17850744
- DOI: 10.1016/j.str.2007.06.019
- Structures With Same Primary Citation
- PubMed Abstract:
- X-ray structure of Arabidopsis At2g06050, 12-oxophytodienoate reductase isoform 3
Malone, T.E., Madson, S.E., Wrobel, R.L., Jeon, W.B., Rosenberg, N.S., Johnson, K.A., Bingman, C.A., Smith, D.W., Phillips Jr., G.N., Markley, J.L., Fox, B.G.
(2005) Proteins 58: 243
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 repre ...
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.
Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.