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Protocols

xia2 specifications

Information


Unique identifier OMICS_29334
Name xia2
Software type Application/Script
Interface Command line interface
Restrictions to use None
Output format TXT,HTML
Operating system Unix/Linux
Programming languages Python
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 5.0
Stability Stable
Requirements
CCP4
Maintained Yes

Download


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Versioning


No version available

Documentation


Maintainers


  • person_outline Graeme Winter
  • person_outline xia2 Team

Additional information


http://xia2.blogspot.fr/

Publications for xia2

library_books

Decision making in xia2

2013
PMCID: 3689529
PMID: 23793152
DOI: 10.1107/S0907444913015308

xia2 citations

 (302)
call_split

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

[…] l of these crystals to select the best diffracting part of each crystal. EDNA and iMosflm were used for strategy calculation during data collection. All data sets were processed using the Fast_dp and xia2 packages, which use the programs XDS, POINTLESS and SCALA from the CCP4 suite. Data-collection statistics are given in Table .The best diffracting crystal was formed in one of the additive screen […]

library_books

Substrate bound outward open structure of a Na+ coupled sialic acid symporter reveals a new Na+ site

2018
Nat Commun
PMCID: 5931594
PMID: 29717135
DOI: 10.1038/s41467-018-04045-7

[…] was built using the ARP/wARP web service. The structure from the best-diffracting SeMet-SAD data was determined by PHASER to 1.95 Å resolution in space group C2. The native data set was processed in xia2 through CCP4i and solved to 2.26 Å in space group P22121,. All structures were refined using PHENIX. Data collection and refinement statistics are summarised in Table . In X-ray crystallography, […]

library_books

Targeting a Subpocket in Trypanosoma brucei Phosphodiesterase B1 (TbrPDEB1) Enables the Structure Based Discovery of Selective Inhibitors with Trypanocidal Activity

2018
J Med Chem
PMCID: 5949723
PMID: 29672041
DOI: 10.1021/acs.jmedchem.7b01670

[…] ive was added prior to vitrification. X-ray diffraction data sets were collected at Diamond Light Source (DLS; Didcot, Oxfordshire, UK) beamlines I03 and I04 at 100 K. The data sets were processed by xia2 or autoPROC, which incorporates XDS and AIMLESS, or were integrated using iMOSFLM and reduced using POINTLESS, SCALA, and TRUNCATE, all of which are part of CCP4. […]

library_books

RPAP3 provides a flexible scaffold for coupling HSP90 to the human R2TP co chaperone complex

2018
Nat Commun
PMCID: 5902453
PMID: 29662061
DOI: 10.1038/s41467-018-03942-1

[…] glycerol as a cryo-protectant and the data were collected at Diamond Light source, UK. Wavelength used was 0.9763 Å.The data were processed using standard methodology, and programs of the CCP4 suite, Xia2, REFMAC, BUSTER (https://sbgrid.org/software/titles/buster), and COOT, together with the ARCIMBOLDO software (Supplementary Table ). […]

library_books

Effector gene birth in plant parasitic nematodes: Neofunctionalization of a housekeeping glutathione synthetase gene

2018
PLoS Genet
PMCID: 5919673
PMID: 29641602
DOI: 10.1371/journal.pgen.1007310

[…] h the addition 20% ethylene glycol final concentration) and frozen in a loop in liquid nitrogen. X-ray diffraction data were collected at the Diamond light source beamlines i04-1, processed using the xia2 pipeline [], and the structure was solved by molecular replacement with 3KAL and named Gpa-GSS22-apo. The submitted structure was obtained through an iterative process of manual building and refi […]

library_books

In Silico and Structural Analyses Demonstrate That Intrinsic Protein Motions Guide T Cell Receptor Complementarity Determining Region Loop Flexibility

2018
Front Immunol
PMCID: 5904202
PMID: 29696015
DOI: 10.3389/fimmu.2018.00674

[…] pensing robot (Alpha Biotech Ltd., UK) and data were collected at 100 K at the diamond light source (DLS), Oxfordshire, UK using an ADSC Q315 CCD detector. Reflection intensities were estimated using XIA2 () and the data were analyzed with SCALA and the CCP4 package (). Structures were solved with molecular replacement using PHASER (). Sequences were adjusted with COOT () and the models were refin […]

Citations

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xia2 institution(s)
Diamond Light Source, Didcot, England; Faculty of Life Sciences, University of Manchester, Manchester, England
xia2 funding source(s)
Supported by Diamond Light Source Ltd, the BBSRC through the e-Science pilot project e-HTPX and the EU Sixth Framework through BioXHit and CCP4.

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