9PHP | pdb_00009php

[19-7B AG] 19 bp tensegrity triangle that propagates via blunt-end stacking with A stacking on G at the interface

• PDB DOI: https://doi.org/10.2210/pdb9PHP/pdb
• NAKB: 9PHP

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


• Deposited: 2025-07-09 Released: 2025-08-27 
• 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: 4.33 Å
• R-Value Free: 
  0.204 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.179 (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: 11.56 kDa 
• Atom Count: 773 
• Modeled Residue Count: 38 
• Deposited Residue Count: 38 
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')	A [auth E]	9	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*AP*GP*CP*CP*TP*GP*TP*A)-3')	B [auth A]	10	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*AP*CP*A)-3')	C [auth B]	7	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')	D [auth C]	12	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.33 Å
• R-Value Free:  0.204 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: I 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.02	α = 90
b = 157.02	β = 90
c = 157.02	γ = 90

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: 2025-08-27 
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: 2025-08-27
  Type: Initial release