+Open data
-Basic information
Entry | Database: PDB / ID: 1dcw | ||||||||||||||||||
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Title | STRUCTURE OF A FOUR-WAY JUNCTION IN AN INVERTED REPEAT SEQUENCE. | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / HOLLIDAY JUNCTION / INVERTED REPEAT / FOUR-WAY JUNCTION / DEOXYRIBONUCLEIC ACID | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 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 | 1dcw.cif.gz | 32.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dcw.ent.gz | 22.3 KB | Display | PDB format |
PDBx/mmJSON format | 1dcw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dcw_validation.pdf.gz | 388.3 KB | Display | wwPDB validaton report |
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Full document | 1dcw_full_validation.pdf.gz | 391.3 KB | Display | |
Data in XML | 1dcw_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | 1dcw_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/1dcw ftp://data.pdbj.org/pub/pdb/validation_reports/dc/1dcw | HTTPS FTP |
-Related structure data
Related structure data | 1dcvC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 3045.992 Da / Num. of mol.: 4 / Source method: obtained synthetically #2: Chemical | ChemComp-NA / | #3: 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: 2.24 Å3/Da / Density % sol: 45.05 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: MPD, CACL2, SODIUM CACODYLATE, pH 7.00 | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 7 / Method: unknown | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 8, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30.16 Å / Num. obs: 6322 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 2.7 / % possible all: 96.7 |
Reflection | *PLUS Num. measured all: 18370 |
Reflection shell | *PLUS % possible obs: 96.7 % |
-Processing
Software |
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Refinement | Resolution: 2.1→8 Å / Cross valid method: THROUGHOUT / σ(F): 3 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: 2.1→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.19 Å / Total num. of bins used: 8 /
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.23 / Rfactor Rwork: 0.23 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |