2BY1

Is radiation damage dependent on the dose-rate used during macromolecular crystallography data collection


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Is Radiation Damage Dependent on the Dose-Rate Used During Macromolecular Crystallography Data Collection?

Leiros, H.-K.S.Timmins, J.Ravelli, R.B.G.Mcsweeney, S.M.

(2006) Acta Crystallogr.,Sect.D 62: 125

  • DOI: 10.1107/S0907444905033627
  • Primary Citation of Related Structures:  2BXY, 2BXZ, 2BY0, 2BY2, 2BY3, 2BY5, 2BY6, 2BY7, 2BY8, 2BY9, 2BYA

  • PubMed Abstract: 
  • This paper focuses on the radiation-damage effects when applying the same total X-ray dose to protein crystals at different dose rates. These experiments have been performed on both a selenomethionated protein and on bovine trypsin using dose rates t ...

    This paper focuses on the radiation-damage effects when applying the same total X-ray dose to protein crystals at different dose rates. These experiments have been performed on both a selenomethionated protein and on bovine trypsin using dose rates that span nearly two orders of magnitude. The results show no clear dose-rate effect on the global indicators of radiation damage, but a small measurable dose-rate effect could be found when studying specific radiation damage. It is hypothesized that this observed dose-rate effect relates to differences in the steady-state free-radical concentration.


    Organizational Affiliation

    Macromolecular Crystallography Group, European Synchrotron Radiation Facility (ESRF), 6 Rue Jules Horowitz, 38043 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MALTOOLIGOSYLTREHALOSE TREHALOHYDROLASE
A
602Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)Gene Names: treZ
EC: 3.2.1.141
Find proteins for Q9RX51 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Go to UniProtKB:  Q9RX51
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRE
Query on TRE

Download SDF File 
Download CCD File 
A
TREHALOSE
ALPHA-D-GLUCOPYRANOSYL-ALPHA-D-GLUCOPYRANOSIDE
C12 H22 O11
HDTRYLNUVZCQOY-LIZSDCNHSA-N
 Ligand Interaction
GLC
Query on GLC

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Download CCD File 
A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
BME
Query on BME

Download SDF File 
Download CCD File 
A
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

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Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.608α = 90.00
b = 66.742β = 90.00
c = 153.538γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance