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Protocols

REFMAC5 specifications

Information


Unique identifier OMICS_17736
Name REFMAC5
Alternative names Refinement of Macromolecular Structures, REFMAC
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Version 5.7.0032
Stability Stable
Source code URL https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/SourceEtal/source.html
Maintained Yes

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Publications for Refinement of Macromolecular Structures

REFMAC5 citations

 (2098)
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Structural insights into the nanomolar affinity of RING E3 ligase ZNRF1 for Ube2N and its functional implications

2018
PMCID: 5941314
PMID: 29626159
DOI: 10.1042/BCJ20170909
call_split See protocol

[…] l SAD phasing of the Ube2N : ZNRF1CTD crystal using the SHELX suite [] and the model was built using BUCCANEER []. Subsequent rounds of manual building and refinements were carried out using COOT [], REFMAC5 [], and Phenix.Refine []. […]

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Molecular mechanism of influenza A NS1 mediated TRIM25 recognition and inhibition

2018
Nat Commun
PMCID: 5940772
PMID: 29739942
DOI: 10.1038/s41467-018-04214-8

[…] 5). Subsequently, this solution was fixed and two out of four molecules of NS1-RBD were located with a TFZ score of 18.6. Models were iteratively improved by manual building in Coot and refined using REFMAC5 and Phenix,. All structural figures were prepared in PyMOL. Protein interfaces were calculated using PISA. Coordinates and structure factors were deposited in the Protein Data Bank under acces […]

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NADH/NADPH bi cofactor utilizing and thermoactive ketol acid reductoisomerase from Sulfolobus acidocaldarius

2018
Sci Rep
PMCID: 5940873
PMID: 29739976
DOI: 10.1038/s41598-018-25361-4
call_split See protocol

[…] e chain differences as well as the locations of many solvent molecules. Manual modification of the model was conducted using COOT. Computational refinement used CNS and PHENIX with TLS as well as the Refmac5 in CCP4 program suite. Non-crystallographic symmetry (NCS) restraints were included at the early stages but released in the end due to significant deviations between the two monomers. The atom […]

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Higher order scaffoldin assembly in Ruminococcus flavefaciens cellulosome is coordinated by a discrete cohesin dockerin interaction

2018
Sci Rep
PMCID: 5934362
PMID: 29725056
DOI: 10.1038/s41598-018-25171-8
call_split See protocol

[…] f the heterodimer RfCohScaB5-DocScaA complex were present in the asymmetric unit. The partially obtained model was completed with Buccaneer and with manual modeling in COOT. It was then refined using REFMAC5 and PDB REDO interspersed with model adjustment in COOT. The final round of refinement was performed using the TLS/restrained refinement procedure using each module as a single group, giving t […]

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Identification of a pyrophosphate dependent kinase and its donor selectivity determinants

2018
Nat Commun
PMCID: 5931981
PMID: 29720581
DOI: 10.1038/s41467-018-04201-z
call_split See protocol

[…] ar replacement method with the atomic coordinates of the unliganded TM0415 (PDB ID 1VK4) using the program Molrep. The structures were constructed using the program COOT and refined using the program REFMAC5, with the Translation Libration Screw refinement technique. The statistics for data collections and refinements are summarized in Supplementary Table . […]

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A new crystal form of Aspergillus oryzae catechol oxidase and evaluation of copper site structures in coupled binuclear copper enzymes

2018
PLoS One
PMCID: 5929527
PMID: 29715329
DOI: 10.1371/journal.pone.0196691
call_split See protocol

[…] were then further re-refined: 1BT1, 1BT3, 2AHL, 2P3X, 2ZMZ and 4J6T. Initially, water molecules or oxygen species between coppers were totally omitted, and new electron density maps were calculated. REFMAC5 [] from the CCP4 [] software package was used in refinement. Based on the calculated omit electron density maps, some of the structures were re-refined. No links between copper ions and oxygen […]

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REFMAC5 institution(s)
Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, England
REFMAC5 funding source(s)
This work was supported by the Medical Research Council (grant MC_US_A025_0104).

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