5DO5 | pdb_00005do5

Crystal Structure of 2'-Fluoro-RNA bearing a phosphorodithioate

• PDB DOI: https://doi.org/10.2210/pdb5DO5/pdb
• NAKB: 5DO5

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


• Deposited: 2015-09-10 Released: 2016-09-21 
• Deposition Author(s): Pallan, P.S., Egli, M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.230 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

Crystal Structure of 2'-Fluoro-RNA bearing a phosphorodithioate

Pallan, P.S., Egli, M.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 3.89 kDa 
• Atom Count: 407 
• Modeled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*(AF2)P*(2SG)P*CP*G)-3')	A	12	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.230 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.237	α = 90
b = 34.366	β = 127.5
c = 31.976	γ = 90

Software Package:

Software Name	Purpose
SHELX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-09-21 
Deposition Author(s): Pallan, P.S., Egli, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM086937

Revision History  

• Version 1.0: 2016-09-21
  Type: Initial release
  
• Version 1.1: 2016-10-19
  Changes: Refinement description
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description