PMID: 22681901 , Related PDB id: 4FE1

Authors:

Brunger AT, Adams PD, Fromme P, Fromme R, Levitt M, Schroder GF

Title:

Improving the accuracy of macromolecular structure refinement at 7 A resolution.

Journal:

Structure. 2012 Jun 6;20(6):957-66.

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 A 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 A 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.