+
Open data
-
Basic information
Entry | Database: PDB / ID: 4e7y | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Lambda-[Ru(phen)2(dppz)]2+ Bound to CCGGATCCGG | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / Intercalation / Lambda-[Ru(phen)2(dppz)]2+ | Function / homology | : / Lambda-Ru(phen)2(dppz) complex / DNA | ![]() Method | ![]() ![]() ![]() ![]() Hall, J.P. / Cardin, C.J. | ![]() ![]() Title: Crystal Structure of lambda-[Ru(phen)2(dppz)]2+ with oligonucleotides containing TA/TA and AT/AT steps show two intercalation modes. Authors: Niyazi, H. / Hall, J.P. / O'Sullivan, K. / Winter, G. / Sorensen, T. / Kelly, J.M. / Cardin, C.J. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 19.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 12 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 761.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 766.1 KB | Display | |
Data in XML | ![]() | 4.2 KB | Display | |
Data in CIF | ![]() | 5 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 / Details: DNA Purchased from ATDBio |
---|---|
#2: Chemical | ChemComp-RKP / |
#3: Chemical | ChemComp-BA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.02 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1ul 2mM DNA Oligomer, 1ul 3mM Lambda-[Ru(phen)2(dppz)]2+, 1ul 1mM Lambda-[Ru(tap)2(dppz-(Me)2]2+, 6ul 10% 1-methyl-2,4-pentanediol, 40mM Sodium cacodylate, 12mM Spermeine tetra-HCl, 80mM ...Details: 1ul 2mM DNA Oligomer, 1ul 3mM Lambda-[Ru(phen)2(dppz)]2+, 1ul 1mM Lambda-[Ru(tap)2(dppz-(Me)2]2+, 6ul 10% 1-methyl-2,4-pentanediol, 40mM Sodium cacodylate, 12mM Spermeine tetra-HCl, 80mM Potassium Chloride, 20mM Barium Chloride, equilibrated against 1ml 35% 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2012 |
Radiation | Monochromator: Si(111) dual crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→34.66 Å / Num. all: 4747 / Num. obs: 4747 / % possible obs: 100 % |
Reflection shell | Resolution: 1.7→1.75 Å / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 26.951 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→33.74 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.702→1.746 Å / Total num. of bins used: 20
|