3RZT

Neutron structure of perdeuterated rubredoxin using rapid (14 hours) data


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Rapid visualization of hydrogen positions in protein neutron crystallographic structures.

Munshi, P.Chung, S.L.Blakeley, M.P.Weiss, K.L.Myles, D.A.Meilleur, F.

(2012) Acta Crystallogr D Biol Crystallogr 68: 35-41

  • DOI: https://doi.org/10.1107/S0907444911048402
  • Primary Citation of Related Structures:  
    3RYG, 3RZ6, 3RZT, 3SS2

  • PubMed Abstract: 

    Neutron crystallography is a powerful technique for experimental visualization of the positions of light atoms, including hydrogen and its isotope deuterium. In recent years, structural biologists have shown increasing interest in the technique as it uniquely complements X-ray crystallographic data by revealing the positions of D atoms in macromolecules. With this regained interest, access to macromolecular neutron crystallography beamlines is becoming a limiting step. In this report, it is shown that a rapid data-collection strategy can be a valuable alternative to longer data-collection times in appropriate cases. Comparison of perdeuterated rubredoxin structures refined against neutron data sets collected over hours and up to 5 d shows that rapid neutron data collection in just 14 h is sufficient to provide the positions of 269 D atoms without ambiguity.


  • Organizational Affiliation

    Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rubredoxin54Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: PF1282rub
UniProt
Find proteins for P24297 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore P24297 
Go to UniProtKB:  P24297
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24297
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download Ideal Coordinates CCD File 
B [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.92α = 90
b = 34.87β = 90
c = 43.5γ = 90
Software Package:
Software NamePurpose
LAUEGENdata collection
PHENIXrefinement
LAUEGENdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2012-01-04
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Data collection, Structure summary
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description