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- PDB-6qt2: Radiation damage study on a 16mer DNA segment, structure at 6.2 M... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qt2 | |||||||||||||||||||||||||||||||
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Title | Radiation damage study on a 16mer DNA segment, structure at 6.2 MGy dose | |||||||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / radiation damage / global damage / specific damage | Function / homology | DNA / DNA (> 10) | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Bugris, V. / Harmat, V. / Ferenc, G. / Brockhauser, S. / Carmichael, I. / Garman, E.F. | Funding support | | ![]() ![]()
![]() ![]() Title: Radiation-damage investigation of a DNA 16-mer. Authors: Bugris, V. / Harmat, V. / Ferenc, G. / Brockhauser, S. / Carmichael, I. / Garman, E.F. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 23.6 KB | Display | ![]() |
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PDB format | ![]() | 13.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 375.4 KB | Display | ![]() |
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Full document | ![]() | 376 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 | ![]() 6qt1SC ![]() 6qt3C ![]() 6qt4C ![]() 6qt5C ![]() 6qt6C ![]() 6qt7 S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components on special symmetry positions |
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Components
#1: DNA chain | Mass: 4898.191 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Self complementary model DNA sequence derived from kB33 DNA segment. The present sequence is one nucleotide shorter than that of PDB structure 1SGS Source: (synth.) synthetic construct (others) | ||
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#2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.14 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: 2 microliter 1.5 mM DNA solution (5mM HEPES pH 6.6) plus 2 microliter 10 mM HEPES pH 6.6 plus 4 microliter reservoir solution, against a reservoir of 1 ml 34% PEG200, 600 mM CaCl2 and 10 mM HEPES pH 8.6. PH range: 6.6-8.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 22, 2018 | ||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→31.34 Å / Num. obs: 3879 / % possible obs: 92.5 % / Redundancy: 3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.038 / Rrim(I) all: 0.068 / Net I/σ(I): 8.7 | ||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6QT1 Resolution: 1.8→31.34 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.941 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.168 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. The final model of the lowest dose dataset 6QT1 was further refined against the current dataset collected at higher dose.
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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 max: 113.8 Å2 / Biso mean: 50.011 Å2 / Biso min: 25.33 Å2
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Refinement step | Cycle: final / Resolution: 1.8→31.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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