Tryparedoxin II from C.fasciculata solved by sulphur phasing

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

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De Novo Phasing of Two Crystal Forms of Tryparedoxin II Using the Anomalous Scattering from S Atoms: A Combination of Small Signal and Medium Resolution Reveals This to be a General Tool for Solving Protein Crystal Structures

Micossi, E.Hunter, W.N.Leonard, G.A.

(2002) Acta Crystallogr D Biol Crystallogr 58: 21

  • DOI: https://doi.org/10.1107/s0907444901016808
  • Primary Citation of Related Structures:  
    1O6J, 1O81

  • PubMed Abstract: 

    The de novo phasing of the structures of two crystal forms of tryparedoxin II from Crithidia fasciculata has been carried out using single-wavelength anomalous diffraction techniques exploiting only the small anomalous signal from the S atoms intrinsic to the native protein. Data were collected at 1.77 A wavelength, where the Bijvoet ratio is approximately 1.2%. Data collected to d(min) = 2.5 A from a crystal of form I, which has a diffraction limit of d(min) = 1.5 A and a solvent content of approximately 46%, produced readily interpretable electron-density maps. When these phases were extended to the resolution limit of the crystals, almost the entire model could be traced automatically. Crystals of form II have a much higher solvent content, approximately 72%, and a much lower diffraction limit than form I and at 1.77 A wavelength yielded data only to d(min) = 2.7 A. Despite the medium resolution of the data for this crystal form, it was possible both to determine the heavy-atom partial structure and then use it to produce, still at d(min) = 2.7 A, an excellent quality interpretable electron-density map. This was then improved by phase extension to the d(min) = 2.35 A diffraction limits of a different crystal for which data were collected on a more intense beamline. The success of this latter structure solution markedly increases the potential use in macromolecular crystal structure determination of the anomalous signal available from S atoms that occur naturally in proteins and, as is discussed, has significant implications for structure determination in the high-throughput era.

  • Organizational Affiliation

    Macromolecular Crystallography, European Synchrotron Radiation Facility, BP 220, F-38043 Grenoble CEDEX, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
152Crithidia fasciculataMutation(s): 0 
Find proteins for O77093 (Crithidia fasciculata)
Explore O77093 
Go to UniProtKB:  O77093
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO77093
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.7α = 90
b = 111.7β = 90
c = 56.5γ = 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: 2002-12-19
    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: 2017-07-05
    Changes: Refinement description
  • Version 1.4: 2019-10-09
    Changes: Data collection, Derived calculations, Experimental preparation, Other