[English] 日本語
Yorodumi- PDB-1m77: Near Atomic Resolution Crystal Structure of an A-DNA Decamer d(CC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m77 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Near Atomic Resolution Crystal Structure of an A-DNA Decamer d(CCCGATCGGG): Cobalt Hexammine Interactions with A-DNA | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / A-DNA / Cobalt hexammine | Function / homology | COBALT HEXAMMINE(III) / DNA | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | Authors | Ramakrishnan, B. / Sekharudu, C. / Pan, B.C. / Sundaralingam, M. | Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 | Title: Near-atomic resolution crystal structure of an A-DNA decamer d(CCCGATCGGG): cobalt hexammine interaction with A-DNA. Authors: Ramakrishnan, B. / Sekharudu, C. / Pan, B. / Sundaralingam, M. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1m77.cif.gz | 15.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1m77.ent.gz | 8.9 KB | Display | PDB format |
PDBx/mmJSON format | 1m77.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m77_validation.pdf.gz | 385.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1m77_full_validation.pdf.gz | 385.8 KB | Display | |
Data in XML | 1m77_validation.xml.gz | 3 KB | Display | |
Data in CIF | 1m77_validation.cif.gz | 3.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m7/1m77 ftp://data.pdbj.org/pub/pdb/validation_reports/m7/1m77 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically |
---|---|
#2: Chemical | ChemComp-NCO / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.5 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: cobalt hexammine, cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å |
Detector | Type: NICOLET / Detector: AREA DETECTOR / Date: Sep 22, 1993 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→28 Å / Num. all: 7785 / Num. obs: 6929 / % possible obs: 90 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.4 % / Rsym value: 0.055 |
Reflection shell | Resolution: 1.25→1.31 Å / Num. unique all: 433 |
Reflection | *PLUS % possible obs: 90 % / Num. measured all: 51067 / Rmerge(I) obs: 0.055 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: fiber A-DNA Resolution: 1.25→8 Å / Isotropic thermal model: isotropic / σ(F): 2
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→8 Å
| ||||||||||||||||||||
LS refinement shell | Resolution: 1.25→1.31 Å /
| ||||||||||||||||||||
Refine LS restraints | *PLUS
|