+
Open data
-
Basic information
Entry | Database: PDB / ID: 5jeu | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | del-[Ru(phen)2(dppz)]2+ bound to d(TCGGCGCCGA) with Ba2+ | ||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / ruthenium / light-switch / semi-intercalation | Function / homology | Delta-Ru(phen)2(dppz) complex / : / DNA | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Hall, J.P. / Cardin, C.J. | ![]() ![]() Title: Delta chirality ruthenium 'light-switch' complexes can bind in the minor groove of DNA with five different binding modes. Authors: Hall, J.P. / Keane, P.M. / Beer, H. / Buchner, K. / Winter, G. / Sorensen, T.L. / Cardin, D.J. / Brazier, J.A. / Cardin, C.J. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 37 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 26.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 3.6 KB | Display | |
Data in CIF | ![]() | 4.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: DNA chain | Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-BA / | ||||
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.92 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1uL 4mM del-[Ru(phen)2(dppz)]2+, 1uL 2mM d(TCGGCGCCGA), 6uL of a solution containing 40mM Na-cacodylate pH 7, 12mM spermine, 80mM KCl, 20mM BaCl2, 10% (v/v) hexylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 14, 2012 |
Radiation | Monochromator: dual Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8266 Å / Relative weight: 1 |
Reflection | Resolution: 0.97→25.18 Å / Num. obs: 20581 / % possible obs: 96.7 % / Observed criterion σ(F): -3 / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.027 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 0.97→1 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.857 / Mean I/σ(I) obs: 1.9 / % possible all: 97.3 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.97→25.177 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|