1O6J

Tryparedoxin II from C.fasciculata solved by sulphur phasing


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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.,Sect.D 58: 21

  • Primary Citation of Related Structures:  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 intrins ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRYPAREDOXIN II
A, B
150Crithidia fasciculataGene Names: txnII
Find proteins for O77093 (Crithidia fasciculata)
Go to UniProtKB:  O77093
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.201 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 114.200α = 90.00
b = 114.200β = 90.00
c = 102.600γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SHARPphasing
SOLVEphasing
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-11-07
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance