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Nat Methods. 2015 Apr;12(4):361-365. doi: 10.1038/nmeth.3286. Epub 2015 Feb 23.

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

Author information

1
Department of Biochemistry, University of Washington, Seattle, WA, USA.
2
Cyrus Biotechnology, Inc., Seattle, WA, USA.
3
Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA.
4
Center for Structural Systems Biology (CSSB) University Medical Center Eppendorf-Hamburg (UKE), Hamburg, Germany.
5
Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany.
6
Institute of Molecular Biotechnology GmbH (IMBA), Austrian Academy of Sciences, Vienna, Austria.
7
Research Institute of Molecular Pathology (IMP), Vienna, Austria.
8
Department of Chemistry, Emory University, Atlanta, GA 30322.
9
Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
10
Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA.
#
Contributed equally

Abstract

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.

PMID:
25707030
PMCID:
PMC4382417
DOI:
10.1038/nmeth.3286
[Indexed for MEDLINE]
Free PMC Article

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