Brünger A T
Howard Hughes Medical Institute, Yale University, New Haven, CT 06511.
J Mol Biol. 1988 Oct 5;203(3):803-16. doi: 10.1016/0022-2836(88)90211-2.
Crystallographic refinement by simulated annealing with molecular dynamics has been applied to a 2.8 A (1 A = 0.1 nm) resolution X-ray structure of aspartate aminotransferase. Comparison of the refined structure and a structure obtained by combined restrained least-squares refinement and manual re-fitting shows a similar R factor, stereochemistry, and mean difference from the isomorphous replacement phase centroids. Crystallographic refinement by simulated annealing accomplished structural changes and improvements of the electron density maps that were not possible by using restrained least-squares refinement without manual re-fitting. Crystallographic refinement by simulated annealing can generate an ensemble of structures, each of which agrees with the diffraction information. Regions of large variations of the ensemble indicate either erroneously fitted or disordered segments of the macromolecule.
通过模拟退火结合分子动力学进行的晶体学精修已应用于天冬氨酸转氨酶分辨率为2.8埃（1埃 = 0.1纳米）的X射线结构。将精修后的结构与通过联合约束最小二乘精修和手动重新拟合得到的结构进行比较，结果显示二者具有相似的R因子、立体化学以及与同晶置换相位中心的平均差异。通过模拟退火进行的晶体学精修实现了结构变化并改善了电子密度图，而仅使用约束最小二乘精修且不进行手动重新拟合则无法做到这一点。通过模拟退火进行的晶体学精修可以生成一组结构，其中每个结构都与衍射信息相符。该组结构中变化较大的区域表明大分子存在错误拟合或无序片段。
