Improving the Accuracy of Macromolecular Structure Refinement at 7 Å Resolution

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 angstrom 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 angstrom 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.