4FC1

Ultra-high resolution neutron structure of crambin at room-temperature


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.253 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Direct observation of hydrogen atom dynamics and interactions by ultrahigh resolution neutron protein crystallography.

Chen, J.C.Hanson, B.L.Fisher, S.Z.Langan, P.Kovalevsky, A.Y.

(2012) Proc Natl Acad Sci U S A 109: 15301-15306

  • DOI: 10.1073/pnas.1208341109
  • Primary Citation of Related Structures:  
    4FC1

  • PubMed Abstract: 
  • The 1.1 Å, ultrahigh resolution neutron structure of hydrogen/deuterium (H/D) exchanged crambin is reported. Two hundred ninety-nine out of 315, or 94.9%, of the hydrogen atom positions in the protein have been experimentally derived and resolved through nuclear density maps ...

    The 1.1 Å, ultrahigh resolution neutron structure of hydrogen/deuterium (H/D) exchanged crambin is reported. Two hundred ninety-nine out of 315, or 94.9%, of the hydrogen atom positions in the protein have been experimentally derived and resolved through nuclear density maps. A number of unconventional interactions are clearly defined, including a potential O─H…π interaction between a water molecule and the aromatic ring of residue Y44, as well as a number of potential C─H…O hydrogen bonds. Hydrogen bonding networks that are ambiguous in the 0.85 Å ultrahigh resolution X-ray structure can be resolved by accurate orientation of water molecules. Furthermore, the high resolution of the reported structure has allowed for the anisotropic description of 36 deuterium atoms in the protein. The visibility of hydrogen and deuterium atoms in the nuclear density maps is discussed in relation to the resolution of the neutron data.


    Organizational Affiliation

    Department of Chemistry, University of Toledo, Toledo, OH 43606, USA. julian.ch.chen@gmail.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CrambinA46Crambe hispanica subsp. abyssinicaMutation(s): 0 
Gene Names: THI2
UniProt
Find proteins for P01542 (Crambe hispanica subsp. abyssinica)
Explore P01542 
Go to UniProtKB:  P01542
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01542
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.253 
  • R-Value Observed: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 22.795α = 90
b = 18.826β = 90.89
c = 41.042γ = 90
Software Package:
Software NamePurpose
PCSdata collection
CNSrefinement
nCNSrefinement
SHELXrefinement
d*TREKdata reduction
LAUENORMdata scaling
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-19
    Type: Initial release
  • Version 1.1: 2012-10-03
    Changes: Database references
  • Version 1.2: 2018-02-28
    Changes: Data collection
  • Version 1.3: 2018-06-06
    Changes: Data collection