3GDA | pdb_00003gda

Crystal study of d(CACGCG).d(CGCGTG) grwon in presence of stannous chloride

• PDB DOI: https://doi.org/10.2210/pdb3GDA/pdb
• NAKB: 3GDA

• Classification: DNA
• Mutation(s): No 


• Deposited: 2009-02-23 Released: 2009-04-07 
• Deposition Author(s): Mandal, P.K., Venkadesh, S., Gautham, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.266 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of d(CACGCG).d(CGCGTG) grown in presence of SnCl2

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: 262 
• Modeled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*AP*CP*GP*CP*G)-3'	A	6	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*CP*GP*TP*G)-3'	B	6	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.266 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 17.552	α = 90
b = 30.207	β = 90
c = 43.682	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-07 
Deposition Author(s): Mandal, P.K., Venkadesh, S., Gautham, N.

Revision History  

• Version 1.0: 2009-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2016-12-21
  Changes: Structure summary
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references
• Version 1.4: 2024-04-03
  Changes: Refinement description