[English] 日本語
Yorodumi- PDB-1dn5: SOLVATION OF THE LEFT-HANDED HEXAMER D(5BRC-G-5BRC-G-5BRC-G) IN C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dn5 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | SOLVATION OF THE LEFT-HANDED HEXAMER D(5BRC-G-5BRC-G-5BRC-G) IN CRYSTALS GROWN AT TWO TEMPERATURES | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / Z-DNA / DOUBLE HELIX / MODIFIED | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.4 Å | Authors | Chevrier, B. / Dock, A.C. / Hartmann, B. / Leng, M. / Moras, D. / Thuong, M.T. / Westhof, E. | Citation | Journal: J.Mol.Biol. / Year: 1986 | Title: Solvation of the left-handed hexamer d(5BrC-G-5BrC-G-5 BrC-G) in crystals grown at two temperatures. Authors: Chevrier, B. / Dock, A.C. / Hartmann, B. / Leng, M. / Moras, D. / Thuong, M.T. / Westhof, E. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1dn5.cif.gz | 16.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1dn5.ent.gz | 11.6 KB | Display | PDB format |
PDBx/mmJSON format | 1dn5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dn5_validation.pdf.gz | 370.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1dn5_full_validation.pdf.gz | 379.3 KB | Display | |
Data in XML | 1dn5_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 1dn5_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/1dn5 ftp://data.pdbj.org/pub/pdb/validation_reports/dn/1dn5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 2046.893 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 1.51 Å3/Da / Density % sol: 18.54 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 310.00K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 37 ℃ / pH: 6.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 310 K |
---|---|
Detector | Type: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.4→10 Å / Num. all: 5470 / Num. obs: 3765 / Observed criterion σ(F): 2 |
Reflection | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 10 Å / Observed criterion σ(F): 2 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.4→10 Å / Occupancy max: 1 / Occupancy min: 0.47 / σ(F): 2 /
| ||||||||||||
Refine Biso |
| ||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→10 Å
| ||||||||||||
Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||
Refinement | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 10 Å / σ(F): 2 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
|