Atomic-accuracy models from 4.5-angstrom cryo-electron microscopy data with density-guided iterative local refinement

作者：DiMaio, Frank; Song, Yifan; Li, Xueming; Brunner, Matthias J.; Xu, Chunfu; Conticello, Vincent; Egelman, Edward; Marlovits, Thomas C.; Cheng, Yifan; Baker, David^*

来源：Nature Methods, 2015, 12(4): 361-U129.

DOI：10.1038/NMETH.3286

• PROTEIN STRUCTURES
• STRUCTURE VALIDATION
• ELECTRON
• MOLPROBITY
• PHENIX
• SPACE

We describe a general approach for refining protein structure models on the basis of cryo-electron microscopy maps with near-atomic resolution. The method integrates Monte Carlo sampling with local density-guided optimization, Rosetta all-atom refinement and real-space B-factor fitting. In tests on experimental maps of three different systems with 4.5-angstrom resolution or better, the method consistently produced models with atomic-level accuracy largely independently of starting-model quality, and it outperformed the molecular dynamics-based MDFF method. Cross-validated model quality statistics correlated with model accuracy over the three test systems.

• 出版日期2015-4