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ARP/wARP specifications

Information


Unique identifier OMICS_15564
Name ARP/wARP
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input format MTZ
Computer skills Basic
Version 7.6
Stability Stable
Maintained Yes

Maintainer


  • person_outline Anastassis Perrakis

Information


Unique identifier OMICS_15564
Name ARP/wARP
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS
Computer skills Medium
Version 7.6
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Anastassis Perrakis

Publications for ARP/wARP

ARP/wARP citations

 (767)
library_books

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

[…] eplacement with anomalous scattering. Six mercury sites were found and refined with SHARP. The resultant map was improved by threefold non-crystallographic averaging and an initial model was built by ARP/WARP. Subsequent refinement was done with REFMAC. Data collection and refinement statistics are listed in Supplementary Table .Data of human TRIM25 CC-PRYSPRY crystals were collected on ESRF beaml […]

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

[…] ls were merged and scaled using BLEND. SeMet sites were identified and refined with the programs SHELX and SHARP,. The phases were further improved by RESOLVE and an initial model 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 an […]

call_split

RING tetramerization is required for nuclear body biogenesis and PML sumoylation

2018
Nat Commun
PMCID: 5876331
PMID: 29599493
DOI: 10.1038/s41467-018-03498-0
call_split See protocol

[…] phase PML RING. Eight Zn2+ positions were determined by CRUNCH2 using data between 20 and 1.6 Å. An interpretable map was obtained by solvent flattening using program SOLOMON. The autotracing program ARP/wARP was then used to produce a σA-weighted 2Fo-Fc map for further manual model building. REFMAC5 was used for structural refinement. Intermittent manual building implemented in COOT was used to c […]

library_books

Structural insights into the RNA methyltransferase domain of METTL16

2018
Sci Rep
PMCID: 5871880
PMID: 29593291
DOI: 10.1038/s41598-018-23608-8

[…] ystal structures of METTL16_291 were solved by molecular replacement using Phaser and the X-ray crystal structure of human methyltransferase 10 domain containing protein (94% identity, PDB ID: 2h00). ARP/wARP was used to build the initial model, which afterwards was placed inside the unit cell with the ACHESYM server. Manual fitting in the electron density maps was completed in COOT with iterative […]

library_books

Identification of aaNAT5b as a spermine N acetyltransferase in the mosquito, Aedes aegypti

2018
PLoS One
PMCID: 5858766
PMID: 29554129
DOI: 10.1371/journal.pone.0194499

[…] factor dropped to a value of around 0.21 at full resolution for the structures, based upon both the 2Fo–Fc and Fo–Fc electron density maps. Solvent molecules were automatically added and refined with ARP/warp [] and Refmac 5.3. […]

call_split

Phosphorylation decelerates conformational dynamics in bacterial translation elongation factors

2018
Sci Adv
PMCID: 5851678
PMID: 29546243
DOI: 10.1126/sciadv.aap9714
call_split See protocol

[…] stal contained two molecules in the asymmetric unit, and 11 I atoms were placed with occupancy above 90%. The initial phases were of sufficient quality to allow automated building, performed with the ARP/wARP suite to almost completeness (~90% of the structure was built in this way). Structure refinement was performed with BUSTER-TNT () using the default options of the program. In each case, refin […]

Citations

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ARP/wARP institution(s)
Department of Biochemistry, The Netherlands Cancer Institute, Amsterdam, Netherlands; Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, UK
ARP/wARP funding source(s)
Supported by the National Institutes of Health (Grant R01 GM62612), the NWO/CW (VENI 700.55.405), the Wellcome Trust (Grant 064405/Z/01/A) and the European Union BIOXHIT FW6 Integrated Project (Grant LSHG-CT-2003-503420).

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