1N7B

RIP-Radiation-damage Induced Phasing


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.155 

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

  • DOI: 10.1016/s0969-2126(03)00006-6
  • Structures With Same Primary Citation

  • 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 nucleic acids 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
SPM
Query on SPM

Download CCD File 
B, H
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
A, B, E
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.247α = 90
b = 51.154β = 90
c = 70.834γ = 90
Software Package:
Software NamePurpose
ProDCdata collection
XDSdata reduction
SHELXDphasing
SHARPphasing
REFMACrefinement
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description