+Open data
-Basic information
Entry | Database: PDB / ID: 1c9z | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | D232-CGTACG | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / INTERCALATOR / INTERCALATION / DRUG / MAJOR GROOVE | Function / homology | Chem-232 / DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | Authors | Williams, L.D. | Citation | Journal: Curr.Med.Chem. / Year: 2000 | Title: Effects of cationic charge on three-dimensional structures of intercalative complexes: structure of a bis-intercalated DNA complex solved by MAD phasing. Authors: Shui, X. / Peek, M.E. / Lipscomb, L.A. / Gao, Q. / Ogata, C. / Roques, B.P. / Garbay-Jaureguiberry, C. / Wilkinson, A.P. / Williams, L.D. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1c9z.cif.gz | 14.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1c9z.ent.gz | 7.7 KB | Display | PDB format |
PDBx/mmJSON format | 1c9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c9z_validation.pdf.gz | 627.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1c9z_full_validation.pdf.gz | 627.9 KB | Display | |
Data in XML | 1c9z_validation.xml.gz | 2.4 KB | Display | |
Data in CIF | 1c9z_validation.cif.gz | 2.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/1c9z ftp://data.pdbj.org/pub/pdb/validation_reports/c9/1c9z | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
| ||||||||||
Components on special symmetry positions |
|
-Components
#1: DNA chain | Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC |
---|---|
#2: Chemical | ChemComp-232 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6 Details: MPD, SPERMINE, MAGNESIUM CHLORIDE, SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 300K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 300 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: UCSD MARK II / Detector: AREA DETECTOR / Date: Sep 9, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→10 Å / Num. all: 5220 / Num. obs: 4698 / % possible obs: 91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 3.2 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.4→2.51 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.06 / % possible all: 84 |
Reflection | *PLUS Num. all: 4698 / Num. obs: 744 / % possible obs: 91 % / Num. measured all: 5220 / Rmerge(I) obs: 0.0514 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.4→10 Å / σ(F): 4 / σ(I): 2 / Stereochemistry target values: PARKINSON ET AL.
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
| |||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 10 Å / Num. reflection obs: 731 / σ(F): 4 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|