6Y0Y | pdb_00006y0y

Sarcin Ricin Loop, mutant C2666U

• PDB DOI: https://doi.org/10.2210/pdb6Y0Y/pdb
• NAKB: 6Y0Y

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


• Deposited: 2020-02-10 Released: 2021-02-17 
• Deposition Author(s): Ennifar, E., Westhof, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 
  0.139 (Depositor), 0.135 (DCC) 
• R-Value Work: 
  0.125 (Depositor) 
• R-Value Observed: 
  0.126 (Depositor) 

Starting Model: experimental

Literature

Sarcin Ricin Loop, mutant C2666U

Ennifar, E., Westhof, E.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 8.82 kDa 
• Atom Count: 765 
• Modeled Residue Count: 27 
• Deposited Residue Count: 27 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (27-MER)	A	27	synthetic construct

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free:  0.139 (Depositor), 0.135 (DCC) 
• R-Value Work:  0.125 (Depositor) 
• R-Value Observed: 0.126 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 22.48	α = 91.58
b = 27.55	β = 93.61
c = 29.69	γ = 108.31

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-17 
Deposition Author(s): Ennifar, E., Westhof, E.

Revision History  

• Version 1.0: 2021-02-17
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description