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Yorodumi- PDB-1g00: ALTERNATION OF DNA AND SOLVENT LAYERS IN THE A FORM OF D(GGCGCC) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g00 | ||||||||||||||||||
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Title | ALTERNATION OF DNA AND SOLVENT LAYERS IN THE A FORM OF D(GGCGCC) OBTAINED BY ETHANOL CRYSTALLIZATION | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / DOUBLE HELIX / A-DNA / DNA LAYERS | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | Authors | Urpi, L. / Navaza, J. / Subirana, J.A. | Citation | Journal: J.Biomol.Struct.Dyn. / Year: 2000 | Title: Alternation of DNA and solvent layers in the A form of d(GGCGCC) obtained by ethanol crystallization. Authors: Urpi, L. / Navaza, J. / Subirana, J.A. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g00.cif.gz | 26.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g00.ent.gz | 18 KB | Display | PDB format |
PDBx/mmJSON format | 1g00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/1g00 ftp://data.pdbj.org/pub/pdb/validation_reports/g0/1g00 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 1810.205 Da / Num. of mol.: 6 / Source method: obtained synthetically #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.94 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: ethanol, magnesium chloride, sodium cacodylate, tetra-arginine, spermine tetrachloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K | ||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER / Date: Jul 14, 1988 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.297→55.015 Å / Num. all: 3504 / Num. obs: 3504 / % possible obs: 79 % / Observed criterion σ(F): 1 / Redundancy: 1 % / Rmerge(I) obs: 0.0525 |
Reflection shell | Resolution: 2.3→2.45 Å / Redundancy: 1 % / Rmerge(I) obs: 0.274 / Num. unique all: 456 / % possible all: 61.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: A-DNA form fiber Resolution: 2.3→8 Å / Num. parameters: 2801 / Num. restraintsaints: 3093 / σ(I): 2 Stereochemistry target values: Clowney et al. Gelbin et al. Parkinson et al. Details: Used Konnert-Hendrickson conjugate-gradient algorithm instead of the full matrix approach.
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Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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