[English] 日本語
Yorodumi- PDB-1d79: HIGH RESOLUTION REFINEMENT OF THE HEXAGONAL A-DNA OCTAMER D(GTGTA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d79 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | HIGH RESOLUTION REFINEMENT OF THE HEXAGONAL A-DNA OCTAMER D(GTGTACAC) AT 1.4 ANGSTROMS RESOLUTION | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / A-DNA / DOUBLE HELIX | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.45 Å | Authors | Thota, N. / Li, X.H. / Bingman, C.A. / Sundaralingam, M. | Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: High-resolution refinement of the hexagonal A-DNA octamer d(GTGTACAC) at 1.4 A. Authors: Thota, N. / Li, X.H. / Bingman, C.A. / Sundaralingam, M. #1: Journal: Biochemistry / Year: 1991 Title: Hexagonal Crystal Structure of the A-DNA Octamer d(GTGTACAC) and Its Comparison with the Tetragonal Structure: Correlated Variations in Helical Parameters Authors: Jain, S. / Zon, G. / Sundaralingam, M. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1d79.cif.gz | 12.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1d79.ent.gz | 7.9 KB | Display | PDB format |
PDBx/mmJSON format | 1d79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d79_validation.pdf.gz | 358.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1d79_full_validation.pdf.gz | 360.2 KB | Display | |
Data in XML | 1d79_validation.xml.gz | 3 KB | Display | |
Data in CIF | 1d79_validation.cif.gz | 3.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/1d79 ftp://data.pdbj.org/pub/pdb/validation_reports/d7/1d79 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.62 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 283 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 283.00K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 283 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 258 K |
---|---|
Detector | Type: XENTRONICS / Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.45→5 Å / Num. all: 6017 / Num. obs: 3292 / Observed criterion σ(I): 2 |
Reflection | *PLUS Highest resolution: 1.45 Å / Lowest resolution: 5 Å / % possible obs: 67 % / Observed criterion σ(I): 2 / Num. measured all: 9036 / Rmerge(I) obs: 0.052 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.45→5 Å / σ(F): 2 /
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine Biso |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→5 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.45 Å / Lowest resolution: 10 Å / Num. reflection obs: 6017 / σ(F): 2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |