2BY9

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

• PDB DOI: https://doi.org/10.2210/pdb2BY9/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2005-07-29 Released: 2006-02-06 
• Deposition Author(s): Leiros, H.-K.S., Timmins, J., Ravelli, R.B.G., McSweeney, S.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.139 
• R-Value Work: 0.103 
• R-Value Observed: 0.105 

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

• PubMed: 16421442 
• DOI: https://doi.org/10.1107/S0907444905033627
• Primary Citation of Related Structures:  
  2BXY, 2BXZ, 2BY0, 2BY1, 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 25.89 kDa 
• Atom Count: 2,181 
• Modelled Residue Count: 223 
• Deposited Residue Count: 243 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATIONIC TRYPSIN	A [auth X]	243	Bos taurus	Mutation(s): 0  EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus) Explore P00760  Go to UniProtKB:  P00760

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEN	B [auth X]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
SO4	D [auth X], E [auth X]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth X]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	F [auth X]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.139 
• R-Value Work: 0.103 
• R-Value Observed: 0.105 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.245	α = 90
b = 58.323	β = 90
c = 66.735	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-06 
Deposition Author(s): Leiros, H.-K.S., Timmins, J., Ravelli, R.B.G., McSweeney, S.M.

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
• Version 2.0: 2021-08-04
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
• Version 2.1: 2024-11-13
  Changes: Advisory, Data collection, Database references, Structure summary