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 1.4 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: https://doi.org/10.1016/s0969-2126(03)00006-6
  • Primary Citation of Related Structures:  
    1N6X, 1N6Y, 1N7A, 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. 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. [email protected]


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
RNA/DNA (5'-R(*U)-D(P*(BGM))-R(P*AP*GP*GP*U)-3')
A, B, C, D, E
A, B, C, D, E, F, G, H
6N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SPM
Query on SPM
Download Ideal Coordinates CCD File 
Q [auth B],
S [auth H]		SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
K
Query on K
Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth B],
O [auth B],
P [auth B],
R [auth E]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
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

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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: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations