2BY6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.105 
  • R-Value Observed: 0.106 

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 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 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CATIONIC TRYPSINX243Bos taurusMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BAM
Query on BAM

Download CCD File 
X
BENZAMIDINE
C7 H9 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-O
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
X
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
X
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
X
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BAM-TΔS:  3.009999990463257   kJ/mol  BindingDB
BAMΔH:  21.399999618530273   kJ/mol  BindingDB
BAMΔG:  26.700000762939453   kJ/mol  BindingDB
BAMKi:  39000   nM  BindingDB
BAMΔH:  18.899999618530273   kJ/mol  BindingDB
BAMΔG:  26.600000381469727   kJ/mol  BindingDB
BAMΔH:  17   kJ/mol  BindingDB
BAMKi:  21000   nM  BindingDB
BAMΔG:  26.899999618530273   kJ/mol  BindingDB
BAMKi:  4800   nM  BindingDB
BAM-TΔS:  9.90999984741211   kJ/mol  BindingDB
BAM-TΔS:  5.400000095367432   kJ/mol  BindingDB
BAMΔH:  23.700000762939453   kJ/mol  BindingDB
BAM-TΔS:  7.690000057220459   kJ/mol  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.105 
  • R-Value Observed: 0.106 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.262α = 90
b = 58.355β = 90
c = 66.765γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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