2CA6

MIRAS structure determination from hemihedrally twinned crystals


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.165 

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This is version 1.3 of the entry. See complete history


Literature

Detecting and Overcoming Hemihedral Twinning During the Mir Structure Determination of RNA1P.

Hillig, R.C.Renault, L.

(2006) Acta Crystallogr D Biol Crystallogr 62: 750

  • DOI: 10.1107/S0907444906016222
  • Primary Citation of Related Structures:  
    2CA6

  • PubMed Abstract: 
  • The structure of Rna1p was originally solved to 2.7 A resolution by MIRAS from crystals with partial hemihedral twinning in space group I4(1) [Hillig et al. (1999), Mol. Cell, 3, 781-791] by finding a low-twinned native crystal (twin fraction alpha=0.06) and after twin correction of all data sets ...

    The structure of Rna1p was originally solved to 2.7 A resolution by MIRAS from crystals with partial hemihedral twinning in space group I4(1) [Hillig et al. (1999), Mol. Cell, 3, 781-791] by finding a low-twinned native crystal (twin fraction alpha=0.06) and after twin correction of all data sets. Rna1p crystals have now been used to examine how far twinning and twin correction affect MIR phasing with a higher resolution but highly twinned native data set. Even high hemihedral twinning [alphanative=0.39, alphaderivative=0.24] would not have hindered heavy-atom site identification of strong derivatives using difference Patterson maps. However, a weaker derivative could have been missed and refinement would have stalled at high R values had twinning not been identified and accounted for. Twin correction improved both site identification, experimental phasing statistics and MIR map quality. Different strategies were tested for refinement against twinned data. Using uncorrected twinned data and TWIN-CNS, Rna1p has now been refined to 2.2 A resolution (final twinned R and Rfree were 0.165 and 0.218, respectively). The increased resolution enabled release of the NCS restraints and allowed new conclusions to be drawn on the flexibility of the two molecules in the asymmetric unit. In the case of Rna1p, twinned crystal growth was possible owing to the presence of a twofold NCS axis almost parallel to the twin operator.


    Related Citations: 
    • The Crystal Structure of RNA1P: A New Fold for a Gtpase-Activating Protein
      Hillig, R.C., Renault, L., Vetter, I.R., Drell, T., Wittinghofer, A., Becker, J.
      (1999) Mol Cell 3: 781
    • Rangap Mediates GTP Hydrolysis without an Arginine Finger
      Seewald, M.J., Korner, C., Wittinghofer, A., Vetter, I.R.
      (2002) Nature 415: 662

    Organizational Affiliation

    Schering AG Research Laboratories, 13342 Berlin, Germany. roman.hillig@schering.de



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RAN GTPASE-ACTIVATING PROTEIN 1A, B386Schizosaccharomyces pombeMutation(s): 0 
Find proteins for P41391 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P41391 
Go to UniProtKB:  P41391
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.165 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.21α = 90
b = 175.21β = 90
c = 55.85γ = 90
Software Package:
Software NamePurpose
CNXrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-11
    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: 2019-07-24
    Changes: Data collection