6UDN

Crystal Structure of a Self-Assembling DNA Scaffold Containing TA Sticky Ends and Rhombohedral Symmetry


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 

wwPDB Validation 3D Report Full Report



Literature

Crystal Structure of a Self-Assembling DNA Crystal Scaffold with Rhombohedral Symmetry

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

To be published.

Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*AP*CP*TP*GP*AP*CP*TP*CP*AP*TP*GP*CP*TP*CP*AP*TP*CP*TP*GP*A)-3')B21synthetic construct
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*AP*GP*CP*AP*TP*GP*A)-3')A7synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*AP*TP*CP*AP*GP*AP*TP*G)-3')C9synthetic construct
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(P*GP*TP*CP*AP*G)-3')D5synthetic construct
        Small Molecules
        Ligands 1 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        ARS
        Query on ARS

        Download CCD File 
        A, D
        ARSENIC
        As
        RBFQJDQYXXHULB-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.60 Å
        • R-Value Free: 0.256 
        • R-Value Work: 0.234 
        • R-Value Observed: 0.235 
        • Space Group: H 3
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 116.091α = 90
        b = 116.091β = 90
        c = 45.001γ = 120
        Software Package:
        Software NamePurpose
        PHENIXrefinement
        HKL-2000data reduction
        HKL-2000data scaling
        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 Human Genome Research Institute (NIH/NHGRI)United StatesR01GM104960

        Revision History 

        • Version 1.0: 2020-09-23
          Type: Initial release