3TOK | pdb_00003tok

Assaying the energies of biological halogen bonds.

• PDB DOI: https://doi.org/10.2210/pdb3TOK/pdb
• NAKB: 3TOK

• Classification: DNA
• Mutation(s): No 


• Deposited: 2011-09-05 Released: 2012-08-15 
• Deposition Author(s): Carter, M., Ho, P.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 
  0.291 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.289 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Assaying the Energies of Biological Halogen Bonds

Carter, M., Ho, P.S.

(2011) Cryst Growth Des 11: 5087-5095

• DOI: https://doi.org/10.1021/cg200991v

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 6.11 kDa 
• Atom Count: 937 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')	A	10	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*GP*GP*TP*AP*TP*CP*GP*G)-3')	B	10	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.291 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.289 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.36	α = 90
b = 24.6	β = 110.76
c = 37.41	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
EPMR	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-15 
Deposition Author(s): Carter, M., Ho, P.S.

Revision History  

• Version 1.0: 2012-08-15
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description