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 journalArticle

29 Citations (Scopus)

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 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.

Original languageEnglish
Pages (from-to)957-966
Number of pages10
JournalStructure
Volume20
Issue number6
DOIs
Publication statusPublished - Jun 6 2012

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Photosystem I Protein Complex
Synchrotrons
X Ray Crystallography
Electrons

ASJC Scopus subject areas

  • Molecular Biology
  • Structural Biology

Cite this

Brunger, A. T., Adams, P. D., Fromme, P., Fromme, R., Levitt, M., & Schröder, G. F. (2012). Improving the accuracy of macromolecular structure refinement at 7 Å resolution. Structure, 20(6), 957-966. https://doi.org/10.1016/j.str.2012.04.020

Improving the accuracy of macromolecular structure refinement at 7 Å resolution. / Brunger, Axel T.; Adams, Paul D.; Fromme, Petra; Fromme, Raimund; Levitt, Michael; Schröder, Gunnar F.

In: Structure, Vol. 20, No. 6, 06.06.2012, p. 957-966.

Research output: Contribution to journalArticle

Brunger, AT, Adams, PD, Fromme, P, Fromme, R, Levitt, M & Schröder, GF 2012, 'Improving the accuracy of macromolecular structure refinement at 7 Å resolution', Structure, vol. 20, no. 6, pp. 957-966. https://doi.org/10.1016/j.str.2012.04.020
Brunger, Axel T. ; Adams, Paul D. ; Fromme, Petra ; Fromme, Raimund ; Levitt, Michael ; Schröder, Gunnar F. / Improving the accuracy of macromolecular structure refinement at 7 Å resolution. In: Structure. 2012 ; Vol. 20, No. 6. pp. 957-966.
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