X-ray refinement of D2O soaked crystal of concanavalin A

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 

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Direct Determination of the Positions of Deuterium Atoms of Bound Water in Concanavalin a by Neutron Laue Crystallography

Habash, J.Raftery, J.Nuttall, R.Price, H.J.Lehmann, M.S.Wilkinson, C.Kalb(Gilboa), A.J.Helliwell, J.R.

(2000) Acta Crystallogr D Biol Crystallogr 56: 541

  • DOI: https://doi.org/10.1107/s0907444900002353
  • Primary Citation of Related Structures:  
    1C57, 1QNY

  • PubMed Abstract: 

    The correct positions of the deuterium (D) atoms of many of the bound waters in the protein concanavalin A are revealed by neutron Laue diffraction. The approach includes cases where these water D atoms show enough mobility to render them invisible even to ultra-high resolution synchrotron-radiation X-ray crystallography. The positions of the bound water H atoms calculated on the basis of chemical and energetic considerations are often incorrect. The D-atom positions for the water molecules in the Mn-, Ca- and sugar-binding sites of concanavalin A are described in detail.

  • Organizational Affiliation

    Section of Structural Chemistry, Department of Chemistry, University of Manchester, Manchester M13 9PL, England.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CONCANAVALIN A237Canavalia ensiformisMutation(s): 0 
Find proteins for P02866 (Canavalia ensiformis)
Explore P02866 
Go to UniProtKB:  P02866
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02866
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.11α = 90
b = 87.58β = 90
c = 63.26γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-04-30
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other