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- PDB-4rip: BromoUracil substituted structure of intercalation-locked DNA tet... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rip | ||||||||||||||||||||
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Title | BromoUracil substituted structure of intercalation-locked DNA tetraplex | ||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / BromoUracil / homoduplex / intercalation-locked DNA tetraplex | Function / homology | DNA / DNA (> 10) | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Tripathi, S.K. / Zhang, D. / Paukstelis, P. | ![]() ![]() Title: An intercalation-locked parallel-stranded DNA tetraplex. Authors: Tripathi, S. / Zhang, D. / Paukstelis, P.J. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 15.3 KB | Display | ![]() |
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PDB format | ![]() | 9.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 371.6 KB | Display | ![]() |
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Full document | ![]() | 372.4 KB | Display | |
Data in XML | ![]() | 3.1 KB | Display | |
Data in CIF | ![]() | 3.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 3502.962 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.54 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 100 mM MgCl2, 5% PEG400, 30 mM sodium cacodylate, pH 7.4, 8mM cobalt hexamine, VAPOR DIFFUSION, SITTING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 12, 2014 / Details: mirror |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9198 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→55.484 Å / Num. obs: 2699 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 9.5 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 2.9 |
Reflection shell | Resolution: 2.03→2.14 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.196 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.03 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.14 Å
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