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Protocols

CCP4 specifications

Information


Unique identifier OMICS_13635
Name CCP4
Alternative name Collaborative Computational Project 4
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++, Fortran, Python
Computer skills Medium
Version 6.5
Stability Stable
Source code URL http://www.ccp4.ac.uk/download/#os=src
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Collaborative_Computational_Project_Number_4

Subtools


  • Aimless
  • AUSPEX
  • PEAKMAX
  • PHASER
  • SCALA
  • SFALL
  • SORTWATER

Download


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Versioning


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Documentation


Maintainer


  • person_outline Martyn D. Winn

Publications for Collaborative Computational Project 4

CCP4 citations

 (3316)
library_books

Targeting G protein coupled receptor signaling at the G protein level with a selective nanobody inhibitor

2018
Nat Commun
PMCID: 5959942
PMID: 29777099
DOI: 10.1038/s41467-018-04432-0

[…] itial phases for the Gβ1γ1-Nb5 complex were obtained by molecular replacement using the Gβ1γ1-phosducin complex and TssK nanobody nb18 structures as search models (PDB accession: 1A0R, 5M2W) with the CCP4 program PHASER,. Initial models were improved by multiple rounds of REFMAC ver. 5.8 refinement against the Gβ1γ1-Nb5 complex dataset and manual model adjustments with Coot 0.8.8. The final models […]

call_split

Structure guided Discovery of Dual recognition Chemibodies

2018
Sci Rep
PMCID: 5954141
PMID: 29765112
DOI: 10.1038/s41598-018-25848-0
call_split See protocol

[…] thylene glycol and then flash frozen in liquid nitrogen.X-ray diffraction data sets were collected at beamline 502 at Advanced Light Source (ALS) (Berkeley, CA) and processed with programs MOSFLM and SCALA in the CCP4 program suite. The structure was solved to a resolution of 2.77 Å by the molecular replacement program Phaser using a previously reported complex structure of rat DPP-IV with Fab 11A […]

library_books

Structural basis for the recognition of complex type N glycans by Endoglycosidase S

2018
Nat Commun
PMCID: 5951799
PMID: 29760474
DOI: 10.1038/s41467-018-04300-x

[…] ate the previously reported EndoS structure (unmodified PDB 4NUZ) and molecular replacement methods implemented in Phaser and the PHENIX suite. Model rebuilding was carried out with Buccaneer and the CCP4 suite. The final manual building was performed with Coot and refinement with phenix.refine. The structure was validated by MolProbity. Data collection and refinement statistics are presented in S […]

call_split

Vaccine elicited receptor binding site antibodies neutralize two New World hemorrhagic fever arenaviruses

2018
Nat Commun
PMCID: 5951886
PMID: 29760382
DOI: 10.1038/s41467-018-04271-z
call_split See protocol

[…] 8 Fab and the MACV GP1/CR1-07 Fab complex, four copies of the complex were identified per ASU, allowing for electron density modification for phase improvement, which we performed using Parrot in the CCP4 software suite. We decided on resolution cut off by considering completeness of the data, statistically significant CC1/2 and map quality and interpretability. Sample stereo images of electron de […]

call_split

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

[…] Diffraction data were indexed and integrated using XDS followed by scaling and merging in AIMLESS/POINTLESS from the CCP4 software suite []. The anomalous signal of Zn2+ atoms was utilized for initial SAD phasing of the Ube2N : ZNRF1CTD crystal using the SHELX suite [] and the model was bu […]

library_books

The protein kinase CK2 catalytic domain from Plasmodium falciparum: crystal structure, tyrosine kinase activity and inhibition

2018
Sci Rep
PMCID: 5943518
PMID: 29743645
DOI: 10.1038/s41598-018-25738-5

[…] Diffraction data were collected on the PX-III beamline at SLS (Paul Sherrer institute, Villigen, Switzerland) and integrated using XDS. Solvent content analysis using CCP4 indicated the presence of three monomers in the asymmetric unit. The structure was determined using the molecular replacement program PHASER with the hCK2 structure (PDB code: 3NSZ) as a probe. M […]

Citations

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CCP4 institution(s)
STFC Daresbury Laboratory, Daresbury, Warrington, UK; STFC Rutherford Appleton Laboratory, Chilton, Didcot, UK; York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, UK; Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK; MRC Laboratory of Molecular Biology, Hills Road, Cambridge, UK; University of Cambridge Department of Haematology, Cambridge Institute for Medical Research, Hills Road, Cambridge, UK; Biophysical Structural Chemistry, Leiden University, Leiden, Netherlands
CCP4 funding source(s)
This work is supported by the BBSRC through grant BB/F0202281and partly by Wellcome Trust Grant No. 064405/Z/01/A, by the Netherlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) grant No. 700.55.425.

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