4E95 | pdb_00004e95

Lambda-[Ru(TAP)2(dppz-(Me)2)]2+ bound to CCGGATCCGG

• PDB DOI: https://doi.org/10.2210/pdb4E95/pdb
• NAKB: 4E95

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


• Deposited: 2012-03-20 Released: 2013-03-20 
• Deposition Author(s): Hall, J.P., Cardin, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.246 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

The effects of disubstitution on the binding of ruthenium complexes to DNA

Hall, J.P.

(2014) Thesis 

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 3.96 kDa 
• Atom Count: 294 
• Modeled Residue Count: 10 
• Deposited Residue Count: 10 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*CP*GP*GP*AP*TP*CP*CP*GP*G)-3'	A	10	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RML	C [auth A]	(11,12-dimethyldipyrido[3,2-a:2',3'-c]phenazine-kappa~2~N~4~,N~5~)[bis(pyrazino[2,3-f]quinoxaline-kappa~2~N~1~,N~10~)]ruthenium(2+) C40 H26 N12 Ru GGHWDMRPXFPGCU-UHFFFAOYSA-N
BA	B [auth A]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.246 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.44	α = 90
b = 47.44	β = 90
c = 34.53	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
SHELXCD	phasing
SHELXE	model building
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-20 
Deposition Author(s): Hall, J.P., Cardin, C.J.

Revision History  

• Version 1.0: 2013-03-20
  Type: Initial release
  
• Version 1.1: 2017-03-08
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations