Improving the accuracy of macromolecular structure refinement at 7 Å resolution.
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.
Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA. brunger@stanford.edu
Axel T
AT
Brunger
Paul D
PD
Adams
Petra
P
Fromme
Raimund
R
Fromme
Michael
M
Levitt
Gunnar F
GF
Schröder
D001426:Bacterial Proteins / Q000737:chemistry*; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D045331:Photosystem I Protein Complex / Q000737:chemistry*; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012984:Software; D040681:Structural Homology, Protein
D001426:Bacterial Proteins; D045331:Photosystem I Protein Complex