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TitleAtomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement.
Journal, issue, pagesNat Methods, Vol. 12, Issue 4, Page 361-365, Year 2015
Publish dateFeb 23, 2015
AuthorsFrank DiMaio / Yifan Song / Xueming Li / Matthias J Brunner / Chunfu Xu / Vincent Conticello / Edward Egelman / Thomas Marlovits / Yifan Cheng / David Baker /
PubMed AbstractWe 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 ...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-Å 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.
External linksNat Methods / PubMed:25707030 / PubMed Central
MethodsEM (single particle)
Resolution4.1 - 6.0 Å
Structure data

EMDB-6245:
Thermoplasma acidophilum 20S proteasome
Method: EM (single particle) / Resolution: 4.1 Å

EMDB-6246:
Thermoplasma acidophilum 20S proteasome
Method: EM (single particle) / Resolution: 4.4 Å

EMDB-6247:
Thermoplasma acidophilum 20S proteasome
Method: EM (single particle) / Resolution: 5.0 Å

EMDB-6248:
Thermoplasma acidophilum 20S proteasome
Method: EM (single particle) / Resolution: 6.0 Å

Source
  • Thermoplasma acidophilum (acidophilic)

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