1ICK

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

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 2001-04-01 Released: 2001-04-12 
  • Deposition Author(s): Dauter, Z., Adamiak, D.A.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Observed: 0.086 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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 D Biol Crystallogr 57: 990-995

  • DOI: https://doi.org/10.1107/s0907444901006382
  • Primary Citation of Related Structures:  
    1ICK

  • 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 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
MoleculeChains LengthOrganismImage
5'-D(*CP*GP*CP*GP*CP*G)-3'
A, B
6N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Observed: 0.086 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 17.87α = 90
b = 31.55β = 90
c = 44.58γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-04-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description