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Protocols

XDS specifications

Information


Unique identifier OMICS_29335
Name XDS
Alternative names X-ray Detector Software, XDSAPP, XDSAPP2.0
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Output format ASCII,CBF
Operating system Unix/Linux, Mac OS
Parallelization OpenMP
Computer skills Advanced
Version 20180126
Stability Stable
Maintained Yes

Subtools


  • COLSPOT
  • CORRECT
  • DEFPIX
  • IDXREF
  • INIT
  • INTEGRATE
  • XPLAN
  • XYCORR

Download


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Versioning


No version available

Maintainer


  • person_outline Wolfgang Kabsch

Additional information


http://xds.mpimf-heidelberg.mpg.de/html_doc/XDS.html The application can be modified by addition of dedicated modules: XDS-viewer to visualize rotation data and control images and XDSi furnishes a graphical interface to XDS.

Publications for X-ray Detector Software

library_books

XDSAPP2.0

2016 J Appl Crystallogr
DOI: 10.1107/S1600576716004416
library_books

XDS

2010
PMCID: 2815665
PMID: 20124692
DOI: 10.1107/S0907444909047337

XDS citations

 (2038)
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

[…] X-ray data collection of the Gβ1γ1-Nb5 complex was performed at −173 °C. Diffraction data were collected at the NE-CAT-24-ID-E beamline. Data were integrated with XDS and scaled using XSCALE. Initial 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 a […]

call_split

X ray structure of a carpet like antimicrobial defensin–phospholipid membrane disruption complex

2018
Nat Commun
PMCID: 5958116
PMID: 29773800
DOI: 10.1038/s41467-018-04434-y
call_split See protocol

[…] citrate-citric acid pH 5.9. Crystals were flash-cooled at 100 K in mother liquor supplemented with 20% ethylene glycol, and data were collected at the Australian Synchrotron (MX2) and processed using XDS. The structure was solved by molecular replacement with PHASER using the structure of NaD1 in its dimeric form as a search model. The final model was built with Coot and refined with Phenix to a r […]

call_split

Ratchet free solid state inertial rotation of a guest ball in a tight tubular host

2018
Nat Commun
PMCID: 5954156
PMID: 29765050
DOI: 10.1038/s41467-018-04325-2
call_split See protocol

[…] 2M-F PAD detectors at the KEK Photon Factory. Temperature was controlled by the cooling device developed in KEK Photon Factory with dry nitrogen gas flow. The diffraction data were processed with the XDS software program. The structure was solved by direct method and refined by full-matrix least-squares on F2 using the SHELXL-2014/7 program suite running with the Yadokari-XG 2009 software program. […]

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

[…] hoton-counting area detector (2000 Hz max. frame rate) at the microfocus PROXIMA 2—A beamline (λ = 0.9801 Å—SOLEIL, France, see Supplementary Table  for details). Data were integrated and scaled with XDS following standard procedures. […]

call_split

Structural basis of actin monomer re charging by cyclase associated protein

2018
Nat Commun
PMCID: 5951797
PMID: 29760438
DOI: 10.1038/s41467-018-04231-7
call_split See protocol

[…] ne with Pilatus3 6M detector. A complete data set was obtained at 0.97 Å wavelength with 0.1° oscillation angle per diffraction image with a total of 1400 images collected. Data were integrated using X-ray Detector Software, merged and scaled with AIMLESS (CCP4). The initial molecular replacement solution of 1:1 complex CARP-domain and actin was obtained with BALBES program, part of CCP4 suit, giv […]

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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

[…] ected X-ray diffraction data at a wavelength of 0.979 and temperature of 100 K on NE-CAT APS beamline 24-ID-E at the advanced photon source (APS, Argonne National Laboratory). We processed data using XDS and XSCALE, and determined the structure of the complex by molecular replacement with PHASER using JUNV GP1 (PBD: 5EN2) as a search model and BALBES to identify the Fab fragments. We concentrated […]

Citations

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XDS institution(s)
Max-Planck-Institut fur Medizinische Forschung, Abteilung Biophysik, Heidelberg, Germany

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