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Open data
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Basic information
Entry | Database: PDB / ID: 4.0E+95 | ||||||||||||||||||||
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Title | Lambda-[Ru(TAP)2(dppz-(Me)2)]2+ bound to CCGGATCCGG | ||||||||||||||||||||
![]() | 5'-D(*![]() DNA / Intercalation / Photoreactive / Lambda-[Ru(TAP)2(dppz-(Me)2]2+ | Function / homology | : / Chem-RML / DNA | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Hall, J.P. / Cardin, C.J. | ![]() ![]() Title: The effects of disubstitution on the binding of ruthenium complexes to DNA Authors: Hall, J.P. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 19.3 KB | Display | ![]() |
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PDB format | ![]() | 11.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA Purchased from ATDBio / Source: (synth.) synthetic construct (others) |
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#2: Chemical | ChemComp-BA / |
#3: Chemical | ChemComp-RML / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.43 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 1ul 2mM DNA, 1ul 4mM lambda-[Ru(TAP)2(dppz-(Me)2]Cl2, 6ul 10% 2-methyl-2,4-pentanediol, 40mM sodium cacodylate, 12mM spermine tetra-HCl, 80mM potassium chloride, 20mM barium chloride, VAPOR ...Details: 1ul 2mM DNA, 1ul 4mM lambda-[Ru(TAP)2(dppz-(Me)2]Cl2, 6ul 10% 2-methyl-2,4-pentanediol, 40mM sodium cacodylate, 12mM spermine tetra-HCl, 80mM potassium chloride, 20mM barium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2012 |
Radiation | Monochromator: Dual crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→34.53 Å / Num. all: 3219 / Num. obs: 3216 / % possible obs: 99.9 % |
Reflection shell | Resolution: 1.94→1.99 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.236 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→33.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→1.99 Å / Total num. of bins used: 20
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