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PDB_REDO specifications

Information


Unique identifier OMICS_18134
Name PDB_REDO
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained No

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Publications for PDB_REDO

PDB_REDO citations

 (93)
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

[…] dimer RfCohScaB5-DocScaA complex were present in the asymmetric unit. The partially obtained model was completed with Buccaneer and with manual modeling in COOT. It was then refined using REFMAC5 and PDB REDO interspersed with model adjustment in COOT. The final round of refinement was performed using the TLS/restrained refinement procedure using each module as a single group, giving the final mod […]

library_books

A new crystal form of Aspergillus oryzae catechol oxidase and evaluation of copper site structures in coupled binuclear copper enzymes

2018
PLoS One
PMCID: 5929527
PMID: 29715329
DOI: 10.1371/journal.pone.0196691

[…] us crystal structure of AoCO4. In this structure, a bound dioxygen species was observed between the copper ions []. The published structure was refined with dioxygen with Cu-O distances of 2.0–2.6 Å. PDB_REDO-calculated electron density maps also suggested the presence of diatomic oxygen species. However, our new interpretation is that the structure should be refined with peroxide (or hydroperoxid […]

library_books

Cryptic glucocorticoid receptor binding sites pervade genomic NF κB response elements

2018
Nat Commun
PMCID: 5889392
PMID: 29626214
DOI: 10.1038/s41467-018-03780-1

[…] der Contract No. W-31-109-Eng-38. Structures were solved by molecular replacement using PHASER and refined with phenix.refine in the PHENIX suite. Coot was used for visualization model rebuilding and PDB_REDO was used for validation and model improvement,. Figures were generated in MacPyMOL v1.7.0.3 (Schrödinger LLC). Sample electron density for all structures is reported in Supplementary Figure . […]

library_books

Discovery and Characterization of ZUFSP/ZUP1, a Distinct Deubiquitinase Class Important for Genome Stability

2018
Mol Cell
PMCID: 5896202
PMID: 29576527
DOI: 10.1016/j.molcel.2018.02.023

[…] t with COOT () and REFAMC5 () (). The anomalous and native datasets were sufficiently isomorphous to allow refinement of the model against the native dataset. The final structure was re-refined using PDB-REDO (Joosten, R.P. et al., 2014). The final data collection and refinement statistics for the ZUFSP-Ub-Prg complex structure is shown in . All the figures were made using PyMOL (http://pymol.org) […]

library_books

Structural Basis for the Specific Neutralization of Stx2a with a Camelid Single Domain Antibody Fragment

2018
Toxins
PMCID: 5869396
PMID: 29494518
DOI: 10.3390/toxins10030108

[…] 2506.815). From here, refinement cycles using the maximum likelihood target function cycles of phenix.refine [] were alternated with manual building using Coot []. During the refinement process, the PDB_REDO server [] and BUSTER [] was also employed. The final refinement cycle included TLS (Translation/Libration/Screw) refinement, for which the optimal TLS groups were determined using the TLSMD W […]

library_books

Distributed computing for macromolecular crystallography

2018
Acta Crystallogr D Struct Biol
PMCID: 5947778
PMID: 29533240
DOI: 10.1107/S2059798317014565

[…] ng density map could be interpreted using automated model building with the ARP/wARP server (Langer et al., 2008) or Buccaneer (Cowtan, 2006). Another example of a crystallographic server is given by PDB_REDO (Joosten et al., 2014) for the final refinement and validation of solved structures. CCP4 includes several tools for automated structure solution. The molecular-replacement (MR) pipeline BALB […]

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PDB_REDO institution(s)
Department of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
PDB_REDO funding source(s)
Supported from the Netherlands Organization for Scientific Research (NWO) Vidi grant 723.013.003; by Horizon 2020 programmes WestLife (e-Infrastructure Virtual Research Environment project No. 675858) and iNEXT (project No. 653706).

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