Improving the accuracy of macromolecular structure refinement at 7 Å resolution

Brunger, A.T.; Schröder, G.F.; Fromme, P.; Adams, P.D.; Fromme, R.; Levitt, M.

doi:10.1016/j.str.2012.04.020

Journal Article

PreJuSER-111909

Improving the accuracy of macromolecular structure refinement at 7 Å resolution

Brunger, A. T. ; Adams, P. D. ; Fromme, P. ; Fromme, R. ; Levitt, M. ; Schröder, G. F.FZJ*

2012
Elsevier Science London [u.a.]

Structure 20, 957 - 966 (2012) [10.1016/j.str.2012.04.020]

This record in other databases:

Please use a persistent id in citations: doi:10.1016/j.str.2012.04.020

Abstract: In X-ray crystallography, molecular replacement and subsequent refinement is challenging at low resolution. We compared refinement methods using synchrotron diffraction data of photosystem I at 7.4 Å resolution, starting from different initial models with increasing deviations from the known high-resolution structure. Standard refinement spoiled the initial models, moving them further away from the true structure and leading to high R(free)-values. In contrast, DEN refinement improved even the most distant starting model as judged by R(free), atomic root-mean-square differences to the true structure, significance of features not included in the initial model, and connectivity of electron density. The best protocol was DEN refinement with initial segmented rigid-body refinement. For the most distant initial model, the fraction of atoms within 2 Å of the true structure improved from 24% to 60%. We also found a significant correlation between R(free) values and the accuracy of the model, suggesting that R(free) is useful even at low resolution.

Keyword(s): Bacterial Proteins: chemistry (MeSH) ; Crystallography, X-Ray (MeSH) ; Models, Molecular (MeSH) ; Photosystem I Protein Complex: chemistry (MeSH) ; Protein Structure, Secondary (MeSH) ; Protein Structure, Tertiary (MeSH) ; Software (MeSH) ; Structural Homology, Protein (MeSH) ; Bacterial Proteins ; Photosystem I Protein Complex