2CA6

MIRAS structure determination from hemihedrally twinned crystals


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


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.,Sect.D 62: 750

  • DOI: 10.1107/S0907444906016222

  • 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 ...

    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: 
    • Rangap Mediates GTP Hydrolysis without an Arginine Finger
      Seewald, M.J.,Korner, C.,Wittinghofer, A.,Vetter, I.R.
      (2002) Nature 415: 662
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RAN GTPASE-ACTIVATING PROTEIN 1
A, B
386Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rna1
Find proteins for P41391 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P41391
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.165 
  • Space Group: I 41
Unit Cell:
Length (Å)Angle (°)
a = 175.210α = 90.00
b = 175.210β = 90.00
c = 55.850γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
CNXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-11
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-07-24
    Type: Data collection