3HGA | pdb_00003hga

Crystal Structure of 4-Se-Uridine Derivatized RNA

• PDB DOI: https://doi.org/10.2210/pdb3HGA/pdb
• NAKB: 3HGA

• Classification: RNA
• Mutation(s): No 


• Deposited: 2009-05-13 Released: 2009-08-18 
• Deposition Author(s): Sheng, J., Soares, A., Huang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.243 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Oxygen Replacement with Selenium at the Uridine 4-Position for RNA Structure Study and Visualization

Sheng, J., Soares, A., Huang, Z.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 1.93 kDa 
• Atom Count: 157 
• Modeled Residue Count: 6 
• Deposited Residue Count: 6 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*UP*(US5)P*CP*GP*CP*G)-3'	A [auth X]	6	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.243 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.255	α = 90
b = 34.079	β = 90
c = 28.931	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
PHASES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-18 
Deposition Author(s): Sheng, J., Soares, A., Huang, Z.

Revision History  

• Version 1.0: 2009-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2012-02-29
  Changes: Structure summary
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2018-01-24
  Changes: Database references
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references, Derived calculations