3SD8 | pdb_00003sd8

Crystal structure of Ara-FHNA decamer DNA

• PDB DOI: https://doi.org/10.2210/pdb3SD8/pdb
• NAKB: 3SD8

• Classification: DNA
• Mutation(s): No 


• Deposited: 2011-06-08 Released: 2012-08-29 
• Deposition Author(s): Egli, M., Pallan, P.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 
  0.238 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Structural Origins of Opposite Effects on Stability by Axial and Equatorial 3'-Fluoro Modifications of Hexitol Nucleic Acid (HNA)

Egli, M., Pallan, P.S., Allerson, C.R., Prakash, T.P., Berdeja, A., Yu, J., Bhat, B., Swayze, E.E., Seth, P.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 6.24 kDa 
• Atom Count: 438 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*GP*TP*AP*(F4H)P*AP*CP*GP*C)-3'	A, B	10	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SR	C [auth A]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free:  0.238 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.003	α = 90
b = 42.855	β = 90
c = 45.833	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-29 
Deposition Author(s): Egli, M., Pallan, P.S.

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description