9C6H | pdb_00009c6h

[d3] Tensegrity triangle with deazapurine center strand (strand 3) in R3

• PDB DOI: https://doi.org/10.2210/pdb9C6H/pdb
• NAKB: 9C6H

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


• Deposited: 2024-06-07 Released: 2025-07-30 
• Deposition Author(s): Vecchioni, S., Sha, R., Ohayon, Y., Galindo, M., Lopez-Chamorro, C., Jong, M.
• 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: 4.18 Å
• R-Value Free: 
  0.253 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Deazapurine DNA Nanostructures

Vecchioni, S.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.79 kDa 
• Atom Count: 855 
• 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(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*A)-3')	A	12	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*(7DA)P*CP*(7DA)P*CP*CP*(7GU)P*T)-3')	B	7	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')	C	14	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')	D	9	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.18 Å
• R-Value Free:  0.253 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.52	α = 90
b = 107.52	β = 90
c = 88.789	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: 2025-07-30 
Deposition Author(s): Vecchioni, S., Sha, R., Ohayon, Y., Galindo, M., Lopez-Chamorro, C., Jong, M.

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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	2106790
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: 2025-07-30
  Type: Initial release