+Open data
-Basic information
Entry | Database: PDB / ID: 1dcv | ||||||||||||||||||
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Title | B-DNA DECAMER WITH CENTRAL TA DINUCLEOTIDE | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / CENTRAL TA DINUCLEOTIDE / DEOXYRIBONUCLEIC ACID | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | Authors | Eichman, B.F. / Vargason, J.M. / Mooers, B.H.M. / Ho, P.S. | Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 | Title: The Holliday junction in an inverted repeat DNA sequence: sequence effects on the structure of four-way junctions. Authors: Eichman, B.F. / Vargason, J.M. / Mooers, B.H. / Ho, P.S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dcv.cif.gz | 19.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dcv.ent.gz | 12.1 KB | Display | PDB format |
PDBx/mmJSON format | 1dcv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dcv_validation.pdf.gz | 349 KB | Display | wwPDB validaton report |
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Full document | 1dcv_full_validation.pdf.gz | 351 KB | Display | |
Data in XML | 1dcv_validation.xml.gz | 2.5 KB | Display | |
Data in CIF | 1dcv_validation.cif.gz | 3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/1dcv ftp://data.pdbj.org/pub/pdb/validation_reports/dc/1dcv | 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: 3045.993 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 / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.12 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.00 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: unknown | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 15, 1999 / Details: YALE MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→33.81 Å / Num. obs: 2009 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.49→2.58 Å / Redundancy: 3.37 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 3.1 / % possible all: 91.6 |
Reflection | *PLUS Num. measured all: 7532 / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS % possible obs: 91.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IDEAL B-DNA Resolution: 2.5→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 Details: ANISOTROPIC B VALUES WERE APPLIED TO FCALC DURING REFINEMENT IN ORDER TO SCALE FCALC TO FOBS
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Total num. of bins used: 10 /
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