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Crank specifications


Unique identifier OMICS_28068
Name Crank
Alternative name CRANK2
Software type Pipeline/Workflow
Interface Web user interface
Restrictions to use None
Computer skills Basic
Maintained No



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Publication for Crank

Crank citations


Structural analysis of human ARS2 as a platform for co transcriptional RNA sorting

Nat Commun
PMCID: 5923425
PMID: 29703953
DOI: 10.1038/s41467-018-04142-7

[…] ethionine data sets were selected using a genetic algorithm that maximised the anomalous signal while retaining acceptable merging R-values. These data sets were merged in XSCALE and submitted to the CRANK2 pipeline in combination with the native data set for substructure determination and phasing by SIRAS. The resulting map was used for automatic model building with BUCCANEER followed by iterativ […]


RING tetramerization is required for nuclear body biogenesis and PML sumoylation

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

[…] and subsequently processed, integrated and scaled using MOSFLM/SCALA. The statistics of the data collection are shown in Supplementary Table . Single wavelength dispersion (SAD) method implemented in CRANK2 was used to 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 a […]


Structures of Teneurin adhesion receptors reveal an ancient fold for cell cell interaction

Nat Commun
PMCID: 5851990
PMID: 29540701
DOI: 10.1038/s41467-018-03460-0

[…] iation Facility (beamline ID29) at 100 K. To maximise anomalous signal, data were collected at the L-III Pt edge (λ = 1.072 Å). Data were processed as above, but Bijvoet pairs were unmerged (Table ). Crank2, was used to calculate phases and build an initial model. The model was manually improved using Coot and the NHL domain was placed by molecular replacement in Phaser using a modifed polyalanine […]


Crystal structure of the MSMEG_4306 gene product from Mycobacterium smegmatis

PMCID: 5947703
PMID: 29497021
DOI: 10.1107/S2053230X18002236
call_split See protocol

[…] converted to structure factors using CTRUNCATE (French & Wilson, 1978) as implemented in CCP4 (Winn et al., 2011). Using the scaled data, a partial structure solution was obtained using the automated CRANK2 pipeline (Skubák & Pannu, 2013) in CCP4. The structure was then refined using REFMAC5 (Murshudov et al., 2011) from CCP4 and phenix.refine (Afonine et al., 2012) from PHENIX (Adams et al., 2010 […]


Structural basis for the glycosyltransferase activity of the Salmonella effector SseK3

PMCID: 5892559
PMID: 29449376
DOI: 10.1074/jbc.RA118.001796
call_split See protocol

[…] lographic symmetry was applied to locate the corresponding helices in the asymmetric unit. The anomalous substructure and the initial model of the asymmetric unit comprising eight helices were fed to CRANK2 () to produce improved maps benefiting from 4-fold averaging and an almost complete model.Complete high-resolution data from for SeMet-labeled crystals of SseK3(14–333) were collected at the Sw […]


Structural and biochemical characterization of the biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminasorum bv. viciae 3841

PLoS One
PMCID: 5806882
PMID: 29425231
DOI: 10.1371/journal.pone.0192736

[…] ata at 0.97919 wavelength to 2.46 Å resolution at the Australian Synchrotron MX2 beamline. The data showed a strong anomalous signal (CCanom > 0.15) to about 2.90 Å and the structure was solved using Crank2 [] which automatically built 884 residues in 19 chains in the C2 spacegroup. The structure was manually rebuilt to give four independent chains in the asymmetric unit which formed a tight tetra […]


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Crank institution(s)
Biophysical Structural Chemistry, Gorlaeus Laboratories, Leiden University, Leiden, The Netherlands
Crank funding source(s)
Supported by the N.W.O.

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