2BXZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 

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Ligand Structure Quality Assessment 


This is version 2.0 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 D Biol Crystallogr 62: 125

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

  • 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 that span nearly two orders of magnitude ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MALTOOLIGOSYLTREHALOSE TREHALOHYDROLASEA602Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: treZDR_0464
EC: 3.2.1.1 (PDB Primary Data), 3.2.1.141 (UniProt)
UniProt
Find proteins for Q9RX51 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Explore Q9RX51 
Go to UniProtKB:  Q9RX51
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranoseB, C2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G92130SN
GlyCosmos:  G92130SN
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLC (Subject of Investigation/LOI)
Query on GLC

Download Ideal Coordinates CCD File 
E [auth A], F [auth A]alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
D [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
BME
Query on BME

Download Ideal Coordinates CCD File 
G [auth A]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900006
Query on PRD_900006
B, CtrehaloseOligosaccharide /  Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.418α = 90
b = 66.529β = 90
c = 152.522γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary