6WSZ

Self-assembly of a 3D DNA crystal lattice (4x5 duplex version) containing the J24 immobile Holliday junction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural and Computational Based Approach for the Creation of a Toolbox of Immobile Holliday Junctions for DNA-directed Self-assembly

Simmons, C.R.MacCulloch, T.Stephanopoulos, N.Yan, H.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*CP*AP*GP*AP*CP*TP*CP*CP*AP*CP*TP*CP*A)-3')A 21synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*AP*GP*TP*CP*T)-3')B 5synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*G)-3')C 9synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-3')D 7synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAC
Query on CAC

Download Ideal Coordinates CCD File 
E [auth C],
F [auth C],
G [auth D]
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.458α = 90
b = 68.458β = 90
c = 60.214γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1360635
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM104960
National Science Foundation (NSF, United States)United StatesNSF2004250

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release