3ULN | pdb_00003uln

X-ray Diffraction Studies of Ring Crystals obtained for d(CACGCG).d(CGCGTG): Stage (iii) Hexagonal plates with intense spots and a depression

• PDB DOI: https://doi.org/10.2210/pdb3ULN/pdb
• NAKB: 3ULN

• Classification: DNA
• Mutation(s): No 


• Deposited: 2011-11-11 Released: 2012-07-25 
• Deposition Author(s): Mandal, P.K., Venkadesh, S., Gautham, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 
  0.277 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Starting Model: in silico

Literature

Ring crystals of oligonucleotides: Growth stages and X-ray diffraction studies

Mandal, P.K., Chandrasekaran, A.R., Madhanagopal, B.R., Venkadesh, S., Gautham, N.

(2012) J Cryst Growth 354: 20-26

• DOI: https://doi.org/10.1016/j.jcrysgro.2012.05.029

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 2.44 kDa 
• Atom Count: 168 
• Modeled Residue Count: 8 
• Deposited Residue Count: 8 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
6-mer DNA	A, B	4	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free:  0.277 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 17.816	α = 90
b = 17.816	β = 90
c = 43.006	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-25 
Deposition Author(s): Mandal, P.K., Venkadesh, S., Gautham, N.

Revision History  

• Version 1.0: 2012-07-25
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references
• Version 1.2: 2024-04-03
  Changes: Refinement description