TY - JOUR
T1 - Improving the accuracy of macromolecular structure refinement at 7 Å resolution
AU - Brunger, Axel T.
AU - Adams, Paul D.
AU - Fromme, Petra
AU - Fromme, Raimund
AU - Levitt, Michael
AU - Schröder, Gunnar F.
N1 - Funding Information:
We thank Thomas White and Henry Chapman for stimulating discussions and critical reading of the manuscript, and Corie Ralston for support at beamline 8.2.2 at ALS. A.T.B. acknowledges support by HHMI, M.L. is supported by award GM063817 from NIH, P.D.A. acknowledges support by the US Department of Energy under contract DE-AC03-76SF00098 and NIH/ NIGMS grant P01GM063210, and R.F. and P.F. acknowledge support by the Center for Bio-Inspired Solar Fuel Production, an Energy Frontier Research Center funded by the Department of Energy (DOE), Office of Basic Energy Sciences (award DE-SC0001016). Experiments were carried out the Advanced Light Source, a National User Facilities operated, respectively, by Stanford University and the University of California on behalf of the DOE, Office of Basic Energy Sciences. A.T.B. and P.D.A. performed calculations, analyzed the results, and wrote the paper. R.F. measured and processed the data at beam line 8.2.2 at ALS. G.F.S., M.L., P.F., and R.F. analyzed the results and wrote the paper.
PY - 2012/6/6
Y1 - 2012/6/6
N2 - 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 Rfree, 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.
AB - 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 Rfree, 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.
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U2 - 10.1016/j.str.2012.04.020
DO - 10.1016/j.str.2012.04.020
M3 - Article
C2 - 22681901
AN - SCOPUS:84861965030
SN - 0969-2126
VL - 20
SP - 957
EP - 966
JO - Structure
JF - Structure
IS - 6
ER -