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Yorodumi- PDB-1d76: CRYSTAL AND MOLECULAR STRUCTURE OF A DNA FRAGMENT CONTAINING A 2-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d76 | ||||||||||||||||||
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Title | CRYSTAL AND MOLECULAR STRUCTURE OF A DNA FRAGMENT CONTAINING A 2-AMINO ADENINE MODIFICATION: THE RELATIONSHIP BETWEEN CONFORMATION, PACKING, AND HYDRATION IN Z-DNA HEXAMERS | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / Z-DNA / DOUBLE HELIX / MODIFIED | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.3 Å | Authors | Schneider, B. / Ginell, S.L. / Jones, R. / Gaffney, B. / Berman, H.M. | Citation | Journal: Biochemistry / Year: 1992 | Title: Crystal and molecular structure of a DNA fragment containing a 2-aminoadenine modification: the relationship between conformation, packing, and hydration in Z-DNA hexamers. Authors: Schneider, B. / Ginell, S.L. / Jones, R. / Gaffney, B. / Berman, H.M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d76.cif.gz | 17.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d76.ent.gz | 10.7 KB | Display | PDB format |
PDBx/mmJSON format | 1d76.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d76_validation.pdf.gz | 355.1 KB | Display | wwPDB validaton report |
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Full document | 1d76_full_validation.pdf.gz | 359.4 KB | Display | |
Data in XML | 1d76_validation.xml.gz | 3 KB | Display | |
Data in CIF | 1d76_validation.cif.gz | 3.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/1d76 ftp://data.pdbj.org/pub/pdb/validation_reports/d7/1d76 | 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: 1810.205 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: 1.73 Å3/Da / Density % sol: 27.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, temperature 277.00K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: sitting drop / Details: hanging drop also O. K. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Ambient temp details: ROOM TEMPERATURE |
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Diffraction source | Source: ROTATING ANODE |
Detector | Type: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.02→45 Å / Num. all: 13324 / Num. obs: 5790 / Observed criterion σ(I): 2 |
Reflection | *PLUS Highest resolution: 1.02 Å / Observed criterion σ(I): 2 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||||||
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Refinement | Resolution: 1.3→8 Å / σ(F): 4 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 1.3→8 Å
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Refinement | *PLUS Highest resolution: 1.3 Å / Lowest resolution: 8 Å / σ(F): 4 / Rfactor obs: 0.138 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS |