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Yorodumi- PDB-309d: A DNA DECAMER WITH A STICKY END: THE CRYSTAL STRUCTURE OF D-CGACGATCGT -
+Open data
-Basic information
Entry | Database: PDB / ID: 309d | |||||||||||||||||||||
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Title | A DNA DECAMER WITH A STICKY END: THE CRYSTAL STRUCTURE OF D-CGACGATCGT | |||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / OVERHANGING BASES / CONTINUOUS HELIX | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | Authors | Qiu, H.X. / Dewan, J.C. / Seeman, N.C. | Citation | Journal: J.Mol.Biol. / Year: 1997 | Title: A DNA decamer with a sticky end: the crystal structure of d-CGACGATCGT. Authors: Qiu, H. / Dewan, J.C. / Seeman, N.C. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 309d.cif.gz | 20 KB | Display | PDBx/mmCIF format |
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PDB format | pdb309d.ent.gz | 12.7 KB | Display | PDB format |
PDBx/mmJSON format | 309d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 309d_validation.pdf.gz | 322.6 KB | Display | wwPDB validaton report |
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Full document | 309d_full_validation.pdf.gz | 323 KB | Display | |
Data in XML | 309d_validation.xml.gz | 1.4 KB | Display | |
Data in CIF | 309d_validation.cif.gz | 2.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/09/309d ftp://data.pdbj.org/pub/pdb/validation_reports/09/309d | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3045.004 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.65 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 291K | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 153 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU AFC-5R / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.6 Å / Num. obs: 1768 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.6→3.6 Å / % possible all: 75 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→8 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
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Refine LS restraints |
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Software | *PLUS Name: NUCLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 8 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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