Structure
Volume 20, Issue 6, 6 June 2012, Pages 957-966
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Ways & Means
Improving the Accuracy of Macromolecular Structure Refinement at 7 Å Resolution

https://doi.org/10.1016/j.str.2012.04.020Get rights and content
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Summary

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 Rfree-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 Rfree values and the accuracy of the model, suggesting that Rfree is useful even at low resolution.

Highlights

► Improved models by DEN refinement at 7 Å ► Best method is DEN refinement with initial segmented rigid-body refinement ► Rfree has predictive power at 7 Å

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