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Open data
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Basic information
Entry | Database: PDB / ID: 467d | ||||||||||||||||||
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Title | The structure of a decamer forming a four-way junction | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / G:A MISMATCHES / FOUR-WAY-JUNCTION | Function / homology | DNA | ![]() Method | ![]() ![]() ![]() ![]() Ortiz-Lombardia, M. / Coll, M. | ![]() ![]() Title: Crystal structure of a DNA Holliday junction Authors: Ortiz-Lombardia, M. / Gonzalez, A. / Eritja, R. / Aymami, J. / Azorin, F. / Coll, M. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 18.8 KB | Display | ![]() |
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PDB format | ![]() | 12.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 379 KB | Display | ![]() |
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Full document | ![]() | 381.5 KB | Display | |
Data in XML | ![]() | 3.3 KB | Display | |
Data in CIF | ![]() | 4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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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: 3071.005 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 60 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 6.7% MPD, 0.2M MGCL2, 1.0MM DNA DECAMER AGAINST 45% MPD IN DEPOSIT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1998 |
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: 2.16→19.39 Å / Num. all: 2786 / Num. obs: 2786 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.16→2.23 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.137 / Mean I/σ(I) obs: 5.2 / % possible all: 75.5 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 75.5 % |
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Processing
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Refinement | Method to determine structure: ![]() ![]()
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Refinement step | Cycle: LAST / Resolution: 2.16→19.39 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): -3 / % reflection Rfree: 10 % / Rfactor Rwork: 0.24 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |