9NDF | pdb_00009ndf

[5,8,7,P-1] Shifted tensegrity triangle with an (arm,center,arm) distribution of (5,8,7) base pairs, 1 nt sticky ends, and 5' phosphates

• PDB DOI: https://doi.org/10.2210/pdb9NDF/pdb
• NAKB: 9NDF

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2025-02-18 Released: 2025-03-26 
• Deposition Author(s): Horvath, A., Vecchioni, S., Woloszyn, K., Ohayon, Y.P., Sha, R.
• Funding Organization(s): Office of Naval Research (ONR), Department of Energy (DOE, United States), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 5.01 Å
• R-Value Free: 
  0.176 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.127 (Depositor), 0.128 (DCC) 
• R-Value Observed: 
  0.130 (Depositor) 

Starting Model: experimental

Literature

Shifted tensegrity triangles

Horvath, A., Vecchioni, S., Woloszyn, K., Ohayon, Y.P., Sha, R.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 12.8 kDa 
• Atom Count: 861 
• Modeled Residue Count: 42 
• Deposited Residue Count: 42 
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*CP*GP*GP*AP*CP*AP*CP*TP*CP*A)-3')	A	11	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*AP*CP*AP*CP*CP*GP*T)-3')	B	8	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*TP*GP*AP*GP*TP*GP*TP*GP*CP*TP*CP*T)-3')	C [auth D]	13	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*AP*GP*AP*GP*CP*TP*GP*TP*G)-3')	D [auth X]	10	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 5.01 Å
• R-Value Free:  0.176 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.127 (Depositor), 0.128 (DCC) 
• R-Value Observed: 0.130 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.499	α = 90
b = 131.499	β = 90
c = 48.134	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-03-26 
Deposition Author(s): Horvath, A., Vecchioni, S., Woloszyn, K., Ohayon, Y.P., Sha, R.

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Funding Organization	Location	Grant Number
Office of Naval Research (ONR)	United States	N000141912596
Department of Energy (DOE, United States)	United States	DE-SC0007991
National Science Foundation (NSF, United States)	United States	CCF-2106790
National Science Foundation (NSF, United States)	United States	GCR-2317843

Revision History  

• Version 1.0: 2025-03-26
  Type: Initial release