Improving the accuracy of macromolecular structure refinement at 7 Å resolution

Axel T. Brunger; Paul D. Adams; Petra Fromme; Raimund Fromme; Michael Levitt; Gunnar F. Schröder

doi:10.1016/j.str.2012.04.020

Improving the accuracy of macromolecular structure refinement at 7 Å resolution

Axel T. Brunger, Paul D. Adams, Petra Fromme, Raimund Fromme, Michael Levitt, Gunnar F. Schröder

Research output: Contribution to journal › Article › peer-review

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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.

Original language	English (US)
Pages (from-to)	957-966
Number of pages	10
Journal	Structure
Volume	20
Issue number	6
DOIs	https://doi.org/10.1016/j.str.2012.04.020
State	Published - Jun 6 2012

ASJC Scopus subject areas

Structural Biology
Molecular Biology

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10.1016/j.str.2012.04.020

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@article{6e29e14869b749a6b507fd1ad0f7e942,

title = "Improving the accuracy of macromolecular structure refinement at 7 {\AA} resolution",

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 {\AA} 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 {\AA} 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.",

author = "Brunger, {Axel T.} and Adams, {Paul D.} and Petra Fromme and Raimund Fromme and Michael Levitt and Schr{\"o}der, {Gunnar F.}",

note = "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. ",

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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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Improving the accuracy of macromolecular structure refinement at 7 Å resolution

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