3F8O | pdb_00003f8o

Structure of d(CACGCG).d(CGCGTG) with low concentration of PdCl2

• PDB DOI: https://doi.org/10.2210/pdb3F8O/pdb
• NAKB: 3F8O

• Classification: DNA
• Mutation(s): No 


• Deposited: 2008-11-13 Released: 2008-11-25 
• Deposition Author(s): Mandal, P.K., Venkadesh, S., Gautham, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.240 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: in silico

Literature

Crystal structures of d(CACGCG).d(CGCGTG) grown with different metal ions

Mandal, P.K., Venkadesh, S., Gautham, N.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 3.62 kDa 
• Atom Count: 273 
• Modeled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*DCP*DAP*DCP*DGP*DCP*DG)-3')	A	6	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*DCP*DGP*DCP*DGP*DTP*DG)-3')	B	6	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.240 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 17.785	α = 90
b = 30.941	β = 90
c = 44.789	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
AUTOMAR	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-25 
Deposition Author(s): Mandal, P.K., Venkadesh, S., Gautham, N.

Revision History  

• Version 1.0: 2008-11-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references
• Version 1.3: 2024-04-03
  Changes: Refinement description