1N7A

RIP-Radiation-damage Induced Phasing


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 

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
  • 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 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
    MoleculeChainsLengthOrganismImage
    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: 1.20 Å
    • R-Value Free: 0.156 
    • R-Value Work: 0.124 
    • R-Value Observed: 0.125 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 31.233α = 90
    b = 51.102β = 90
    c = 70.651γ = 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