Journal Article

PreJuSER-111912

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Real-space Refinement with DireX: From Global Fitting to Side-chain Improvements

Wang, Z.FZJ* ; Schröder, G. F.FZJ*

2012
Wiley New York, NY

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Please use a persistent id in citations: doi:10.1002/bip.22046

Abstract: Single-particle cryo-electron microscopy (cryo-EM) has become an important tool to determine the structure of large biomolecules and assemblies thereof. However, the achievable resolution varies considerably over a wide range of about 3.5-20 Å. The interpretation of these intermediate- to low-resolution density maps in terms of atomic models is a big challenge and an area of active research. Here, we present our real-space structure refinement program DireX, which was developed primarily for cryo-EM-derived density maps. The basic principle and its main features are described. DireX employs Deformable Elastic Network (DEN) restraints to reduce overfitting by decreasing the effective number of degrees of freedom used in the refinement. Missing or reduced density due to flexible parts of the protein can lead to artifacts in the structure refinement, which is addressed through the concept of restrained grouped occupancy refinement. Furthermore, we describe the performance of DireX in the 2010 Cryo-EM Modeling Challenge, where we chose six density maps of four different proteins provided by the Modeling Challenge exemplifying typical refinement results at a large resolution range from 3 to 23 Å.

Keyword(s): Antigens, Viral: chemistry (MeSH) ; Aquaporins: chemistry (MeSH) ; Capsid Proteins: chemistry (MeSH) ; Chaperonin 10: chemistry (MeSH) ; Chaperonin 60: chemistry (MeSH) ; Cryoelectron Microscopy: methods (MeSH) ; Eye Proteins: chemistry (MeSH) ; Models, Molecular (MeSH) ; Proteins: chemistry (MeSH) ; Software (MeSH) ; Antigens, Viral ; Aquaporins ; Capsid Proteins ; Chaperonin 10 ; Chaperonin 60 ; Eye Proteins ; Proteins ; VP6 protein, Rotavirus ; aquaporin 0 ; J ; Cryo-EM (auto) ; DireX (auto) ; low resolution (auto) ; flexible fitting (auto) ; real-space refinement (auto)

Note: Record converted from VDB: 16.11.2012

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Contributing Institute(s):

1. Strukturbiochemie (ICS-6)

Research Program(s):

1. Funktion und Dysfunktion des Nervensystems (P33)
2. BioSoft: Makromolekulare Systeme und biologische Informationsverarbeitung (P45)

Appears in the scientific report 2012

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Database coverage:
; BIOSIS Previews ; Current Contents - Life Sciences ; JCR ; NCBI Molecular Biology Database ; Nationallizenz ; SCOPUS ; Science Citation Index ; Science Citation Index Expanded ; Thomson Reuters Master Journal List ; Web of Science Core Collection

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