6S7D

Self-complementary duplex DNA containing an internucleoside phosphoroselenolate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Solid-phase synthesis and structural characterisation of phosphoroselenolate-modified DNA: a backbone analogue which does not impose conformational bias and facilitates SAD X-ray crystallography

Conlon, P.F.Eguaogie, O.Wilson, J.J.Sweet, J.S.T.Steinhoegl, J.Hancox, O.Englert, K.Law, C.J.Allman, S.A.Tucker, J.H.R.Hall, J.P.Vyle, J.S.

(2019) Chem Sci --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*(XCI)P*CP*CP*CP*GP*GP*GP*AP*C)-3')A,B10synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPM
Query on SPM

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

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Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
BA
Query on BA

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Download CCD File 
A, B
BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
XCI
Query on XCI
A, B
NON-POLYMERC10 H15 N2 O6 P Se

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.185 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 38.642α = 90.00
b = 38.642β = 90.00
c = 79.307γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
SHELXCDphasing
DIALSdata reduction
xia2data scaling
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited KingdomEP/C00776X/1

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release