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Open data
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Basic information
Entry | Database: PDB / ID: 5ktv | ||||||||||||||||||||
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Title | Mis-pairing of unnatural base Z-G DNA duplex at pH 8.5 | ||||||||||||||||||||
![]() | DNA (5'-D(P*![]() DNA / Unnatural DNA bases / synthetic biology | Function / homology | DNA / DNA (> 10) | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Ahmad Sobri, A.F. / Brady, R.L. | ![]() ![]() Title: Structural Basis of the Mispairing of an Artificially Expanded Genetic Information System Authors: Reichenbach, L.F. / Ahmad Sobri, A.F. / Zaccai, N.R. / Agnew, C. / Burton, N. / Eperon, L.P. / de Ornellas, S. / Eperon, I.C. / Brady, R.L. / Burley, G.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 | ![]() | 25.3 KB | Display | ![]() |
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PDB format | ![]() | 16 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 382.9 KB | Display | ![]() |
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Full document | ![]() | 383 KB | Display | |
Data in XML | ![]() | 3.4 KB | Display | |
Data in CIF | ![]() | 4.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 476dS 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 on special symmetry positions |
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Components
#1: DNA chain | Mass: 3707.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-CA / #3: 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: 44.6 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100mM Sodium Chloride, 20mM Tris pH 8.5, 34% hexylene glycol, |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→33.48 Å / Num. obs: 2550 / % possible obs: 100 % / Redundancy: 11.1 % / Net I/σ(I): 2.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 476D Resolution: 2.35→34.05 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.201 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.384 / ESU R Free: 0.247 / 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: 67.537 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→34.05 Å
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Refine LS restraints |
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