Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Structure. 2012 Jun 6;20(6):957-66. doi: 10.1016/j.str.2012.04.020.
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.
在 X 射线晶体学中，分子置换和随后的精修在低分辨率下具有挑战性。我们比较了使用同步加速器衍射数据对光合系统 I 进行精修的方法，分辨率为 7.4Å，从与已知高分辨率结构偏差越来越大的不同初始模型开始。标准精修破坏了初始模型，使它们进一步偏离真实结构，并导致高 R(free)-值。相比之下，DEN 精修甚至可以改进最遥远的初始模型，这可以通过 R(free)、与真实结构的原子均方根差异、初始模型中未包含的特征的显著性以及电子密度的连通性来判断。最佳方案是 DEN 精修与初始分段刚体精修相结合。对于最遥远的初始模型，真实结构 2Å 范围内的原子分数从 24%提高到 60%。我们还发现 R(free)值与模型准确性之间存在显著相关性，表明即使在低分辨率下，R(free)也很有用。
