4FE1 : Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution

Experimental Technique/Method:X-RAY DIFFRACTION Resolution:4.92 Classification:PHOTOSYNTHESIS Release Date:2012-08-15 Deposition Date:2012-05-29 Revision Date:2012-08-29 Molecular Weight:359700.12 Macromolecule Type:Protein Residue Count:2334 Atom Site Count:23997 DOI:10.2210/pdb4fe1/pdb 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.