Download MendeleyImproving the accuracy of macromolecular structure refinement at 7 A resolution.
Brunger, A.T., Adams, P.D., Fromme, P., Fromme, R., Levitt, M., Schroder, G.F.(2012) Structure 20: 957-966
- PubMed: 22681901
- DOI: https://doi.org/10.1016/j.str.2012.04.020
- Primary Citation of Related Structures:
4FE1 - PubMed 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.
Organizational Affiliation:
Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA. brunger@stanford.edu
