1N6Y

RIP-phasing on Bovine Trypsin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Specific Radiation-Damage Can Be Used To Solve Macromolecular Crystal Structures

Ravelli, R.B.G.Leiros, H.-K.S.Pan, B.Caffrey, M.McSweeney, S.

(2003) Structure 11: 217-224

  • DOI: 10.1016/s0969-2126(03)00006-6
  • Primary Citation of Related Structures:  
    1N6X, 1N7A, 1N6Y, 1N7B

  • PubMed Abstract: 
  • The use of third generation synchrotron sources has led to renewed concern about the effect of ionizing radiation on crystalline biological samples. In general, the problem is seen as one to be avoided. However, in this paper, it is shown that, far from being a hindrance to successful structure determination, radiation damage provides an opportunity for phasing macromolecular structures ...

    The use of third generation synchrotron sources has led to renewed concern about the effect of ionizing radiation on crystalline biological samples. In general, the problem is seen as one to be avoided. However, in this paper, it is shown that, far from being a hindrance to successful structure determination, radiation damage provides an opportunity for phasing macromolecular structures. This is successfully demonstrated for both a protein and an oligonucleotide, by way of which complete models were built automatically. The possibility that, through the exploitation of radiation damage, the phase problem could become less of a barrier to macromolecular crystal structure determination is discussed.


    Organizational Affiliation

    European Molecular Biology Laboratory (EMBL) Grenoble Outstation, 6 rue Jules Horowitz, B.P. 181, F38042 9, Grenoble Cedex, France. ravelli@embl-grenoble.fr



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Trypsinogen, cationicA223Bos taurusMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ABN
Query on ABN

Download Ideal Coordinates CCD File 
E [auth A]BENZYLAMINE
C7 H9 N
WGQKYBSKWIADBV-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.241α = 90
b = 56.752β = 90
c = 66.204γ = 90
Software Package:
Software NamePurpose
ProDCdata collection
SCALAdata scaling
SHELXDphasing
SHARPphasing
REFMACrefinement
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-03-04
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-02-01
    Changes: Structure summary
  • Version 1.4: 2017-10-11
    Changes: Refinement description