1N7A

RIP-Radiation-damage Induced Phasing


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.124 

wwPDB Validation 3D Report Full Report


This is version 1.3 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

  • Primary Citation of Related Structures:  1N6X, 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 f ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA/DNA (5'-R(*U)-D(P*(BGM))-R(P*AP*GP*GP*U)-3')A,B,C,D,E,F,G,H6N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, E
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SPM
Query on SPM

Download SDF File 
Download CCD File 
B, H
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BGM
Query on BGM
A, B, C, D, E, F, G, H
DNA LINKINGC10 H13 Br N5 O7 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.124 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 31.233α = 90.00
b = 51.102β = 90.00
c = 70.651γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
SHARPphasing
XDSdata reduction
SHELXDphasing
ProDCdata collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-04
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description