6DWT

Crystal structure of double-stranded DNA GAGGCCTC, crystals grown in Mg2+

• PDB DOI: https://doi.org/10.2210/pdb6DWT/pdb
• NAKB: 6DWT

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


• Deposited: 2018-06-27 Released: 2019-01-23 
• Deposition Author(s): Hou, C., Tsodikov, O.V.
• Funding Organization(s): Department of Defense (DOD, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.219 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Literature

Utilizing guanine coordinated Zn2+ to determine DNA crystal structures by single-wavelength anomalous diffraction

Hou, C., Tsodikov, O.V.

(2019) Acta Crystallogr D Biol Crystallogr 75: 32

Biological Assembly 1  

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

Macromolecule Content

• Total Structure Weight: 2.45 kDa 
• Atom Count: 175 
• Modelled Residue Count: 8 
• Deposited Residue Count: 8 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*GP*GP*CP*CP*TP*C)-3')	A	8	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.219 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.255	α = 90
b = 44.255	β = 90
c = 23.597	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-01-23 
Deposition Author(s): Hou, C., Tsodikov, O.V.

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Funding Organization	Location	Grant Number
Department of Defense (DOD, United States)	United States	PC150300P1

Revision History  

• Version 1.0: 2019-01-23
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description