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Open data
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Basic information
Entry | Database: PDB / ID: 4wo3 | |||||||||||||||||||||||||||||||
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Title | THE SECOND C-KIT DNA QUADRUPLEX CRYSTAL STRUCTURE | |||||||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / DNA G-QUADRUPLEX / C/kit | Function / homology | : / DNA / DNA (> 10) | ![]() Biological species | ![]() Method | ![]() ![]() ![]() ![]() Wei, D. / Neidle, S. | Funding support | | ![]()
![]() ![]() Title: THE SECOND C-KIT1 DNA QUADRUPLEX CRYSTAL STRUCTURE Authors: Wei, D. / Neidle, S. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 34.3 KB | Display | ![]() |
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PDB format | ![]() | 24.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 381.4 KB | Display | ![]() |
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Full document | ![]() | 381.9 KB | Display | |
Data in XML | ![]() | 3.3 KB | Display | |
Data in CIF | ![]() | 4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3qxrS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 7028.515 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS. / Source: (synth.) ![]() #2: Chemical | ChemComp-K / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.22 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% MPD, 10 MM MAGNESIUM CHLORIDE, 50 MM POTASSIUM CHLORIDE, AND 50 MM SODIUM CACODYLATE AT PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 283K PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Jul 28, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.73→28.48 Å / Num. obs: 2439 / % possible obs: 94.4 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3QXR Resolution: 2.73→28.48 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.901 / SU B: 16.663 / SU ML: 0.317 / Cross valid method: THROUGHOUT / ESU R Free: 0.428 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.002 Å2
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Refinement step | Cycle: 1 / Resolution: 2.73→28.48 Å
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Refine LS restraints |
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