[English] 日本語
Yorodumi- PDB-233d: THE CRYSTAL STRUCTURE ANALYSIS OF D(CGCGAASSCGCG)2: A SYNTHETIC D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 233d | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | THE CRYSTAL STRUCTURE ANALYSIS OF D(CGCGAASSCGCG)2: A SYNTHETIC DNA DODECAMER DUPLEX CONTAINING FOUR 4'-THIO-2'-DEOXYTHYMIDINE NUCLEOTIDES | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / MODIFIED | Function / homology | DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | Authors | Boggon, T.J. / Hancox, E.L. / McAuley-Hecht, K.E. / Connolly, B.A. / Hunter, W.N. / Brown, T. / Walker, R.T. / Leonard, G.A. | Citation | Journal: Nucleic Acids Res. / Year: 1996 | Title: The crystal structure analysis of d(CGCGAASSCGCG)2, a synthetic DNA dodecamer duplex containing four 4'-thio-2'-deoxythymidine nucleotides. Authors: Boggon, T.J. / Hancox, E.L. / McAuley-Hecht, K.E. / Connolly, B.A. / Hunter, W.N. / Brown, T. / Walker, R.T. / Leonard, G.A. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 233d.cif.gz | 24 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb233d.ent.gz | 16.1 KB | Display | PDB format |
PDBx/mmJSON format | 233d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 233d_validation.pdf.gz | 376.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 233d_full_validation.pdf.gz | 385.8 KB | Display | |
Data in XML | 233d_validation.xml.gz | 6 KB | Display | |
Data in CIF | 233d_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/33/233d ftp://data.pdbj.org/pub/pdb/validation_reports/33/233d | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 3695.524 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: 2.25 Å3/Da / Density % sol: 45.38 % | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, sitting drop / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, SITTING DROP | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 |
---|---|
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.4 Å / Num. obs: 2820 |
Reflection | *PLUS Highest resolution: 2.4 Å / Rmerge(I) obs: 0.065 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.4→8 Å / σ(F): 2 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 8 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |