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- PDB-6qjs: Crystal structure of a DNA dodecamer containing a tetramethylpipe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qjs | |||||||||||||||||||||||||||||||
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Title | Crystal structure of a DNA dodecamer containing a tetramethylpiperidinoxyl (nitroxide) spin label | |||||||||||||||||||||||||||||||
![]() | DNA (5'-D(P*![]() DNA / Nitroxide / Spin label / Tetramethylpiperidinoxyl | Function / homology | COBALT HEXAMMINE(III) / DNA / DNA (> 10) | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Hardwick, J.S. / Haugland, M.M. / Ptchelkine, D. / Brown, T. / Anderson, E.E. | Funding support | | ![]()
![]() ![]() Title: 2'-Alkynyl spin-labelling is a minimally perturbing tool for DNA structural analysis. Authors: Hardwick, J.S. / Haugland, M.M. / El-Sagheer, A.H. / Ptchelkine, D. / Beierlein, F.R. / Lane, A.N. / Brown, T. / Lovett, J.E. / Anderson, E.A. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 27.5 KB | Display | ![]() |
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PDB format | ![]() | 17 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 393.3 KB | Display | ![]() |
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Full document | ![]() | 396.3 KB | Display | |
Data in XML | ![]() | 3.4 KB | Display | |
Data in CIF | ![]() | 3.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qjrC ![]() 1s2rS C: citing same article ( 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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Unit cell |
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Components
#1: DNA chain | Mass: 3870.665 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-NCO / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.4 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Potassium chloride (10 mM), sodium chloride (80 mM), magnesium chloride (20 mM), sodium cacodylate (40 mM, pH 5.5), MPD (35% v/v), Hexammine cobalt(III) chloride (2 mM) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 22, 2017 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.8→37.24 Å / Num. obs: 9926 / % possible obs: 97.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 9.3 | |||||||||||||||
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.589 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1s2r Resolution: 1.8→37.24 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.883 / SU B: 1.849 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.023 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.733 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→37.24 Å
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Refine LS restraints |
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