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Yorodumi- PDB-237d: CRYSTAL STRUCTURE OF A DNA DECAMER SHOWING A NOVEL PSEUDO FOUR-WA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 237d | ||||||||||||||||||
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Title | CRYSTAL STRUCTURE OF A DNA DECAMER SHOWING A NOVEL PSEUDO FOUR-WAY HELIX-HELIX JUNCTION | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / FLIPPED-OUT BASES / INTERMOLECULAR BASE TRIPLET | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | Authors | Spink, N. / Nunn, C.M. / Vojtechovsky, J. / Berman, H.M. / Neidle, S. | Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1995 | Title: Crystal structure of a DNA decamer showing a novel pseudo four-way helix-helix junction. Authors: Spink, N. / Nunn, C.M. / Vojtechovsky, J. / Berman, H.M. / Neidle, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 237d.cif.gz | 14.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb237d.ent.gz | 8.9 KB | Display | PDB format |
PDBx/mmJSON format | 237d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 237d_validation.pdf.gz | 321.9 KB | Display | wwPDB validaton report |
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Full document | 237d_full_validation.pdf.gz | 326 KB | Display | |
Data in XML | 237d_validation.xml.gz | 1.9 KB | Display | |
Data in CIF | 237d_validation.cif.gz | 2.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/37/237d ftp://data.pdbj.org/pub/pdb/validation_reports/37/237d | 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: 3045.005 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.73 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 287.00K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 287 K / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 294 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: XENTRONICS / Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.2 Å / Num. all: 10180 / Num. obs: 1521 |
Reflection | *PLUS Observed criterion σ(I): 0 / Rmerge(I) obs: 0.102 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.5→8 Å / σ(F): 2
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 8 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |