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Yorodumi- PDB-372d: STRUCTURAL VARIABILITY OF A-DNA IN CRYSTALS OF THE OCTAMER D(PCPC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 372d | ||||||||||||||||||||
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Title | STRUCTURAL VARIABILITY OF A-DNA IN CRYSTALS OF THE OCTAMER D(PCPCPCPGPCPGPGPG) | ||||||||||||||||||||
Components | DNA (5'-D(P*Keywords | DNA / A-DNA / DOUBLE HELIX | Function / homology | DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | Authors | Fernandez, L.G. / Subirana, J.A. / Verdaguer, N. / Pyshnyi, D. / Campos, L. | Citation | Journal: J.Biomol.Struct.Dyn. / Year: 1997 | Title: Structural variability of A-DNA in crystals of the octamer d(pCpCpCpGpCpGpGpG) Authors: Fernandez, L.G. / Subirana, J.A. / Verdaguer, N. / Pyshnyi, D. / Campos, L. / Malinina, L. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 372d.cif.gz | 11.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb372d.ent.gz | 6.8 KB | Display | PDB format |
PDBx/mmJSON format | 372d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 372d_validation.pdf.gz | 309.5 KB | Display | wwPDB validaton report |
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Full document | 372d_full_validation.pdf.gz | 309.5 KB | Display | |
Data in XML | 372d_validation.xml.gz | 1 KB | Display | |
Data in CIF | 372d_validation.cif.gz | 1.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/72/372d ftp://data.pdbj.org/pub/pdb/validation_reports/72/372d | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 2428.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.54 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.00 | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-21 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1996 / Details: COLIMATOR 0.4 |
Radiation | Monochromator: GRAFITO / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 733 / % possible obs: 98.2 % / Redundancy: 7.405 % / Rmerge(I) obs: 0.081 |
Reflection shell | Resolution: 2.52→2.62 Å / Rmerge(I) obs: 0.3 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / % possible obs: 98.2 % |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→8 Å / Cross valid method: R-FREE / 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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LS refinement shell | Resolution: 2.6→2.71 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARAM_NDBX.DNA / Topol file: TOP_NDBX.DNA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.181 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_dihedral_angle_deg / Dev ideal: 9.81 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.115 |