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LEFT-HANDED Z-DNA HEXAMER DUPLEX D(CGCGCG)2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Anomalous signal of phosphorus used for phasing DNA oligomer: importance of data redundancy.

Dauter, Z.Adamiak, D.A.

(2001) Acta Crystallogr.,Sect.D 57: 990-995

  • Also Cited By: 5JZQ

  • PubMed Abstract: 
  • The crystal structure of a left-handed Z-DNA hexamer duplex d(CGCGCG)(2) has been solved based on the anomalous diffraction signal of inherent P atoms using data collected at the single wavelength of 1.54 A. The anomalous signal of about 2% of the to ...

    The crystal structure of a left-handed Z-DNA hexamer duplex d(CGCGCG)(2) has been solved based on the anomalous diffraction signal of inherent P atoms using data collected at the single wavelength of 1.54 A. The anomalous signal of about 2% of the total diffracted intensity, constant for all nucleic acids, may be generally useful for solving crystal structures of DNA and RNA oligomers. The multiplicity of intensity measurements is shown to crucially affect the data quality and the ability to solve the phase problem. The anisotropic model refined to an R factor of 8.9% at 0.95 A resolution.


    Organizational Affiliation

    Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute and NSLS, Brookhaven National Laboratory, Building 725A-X9, Upton, NY 11973, USA. dauter@bnl.gov




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*GP*CP*GP*CP*G)-3'A,B6N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPM
Query on SPM

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Download CCD File 
A
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 17.870α = 90.00
b = 31.550β = 90.00
c = 44.580γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-04-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description