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Yorodumi- PDB-6qt3: Radiation damage study on a 16mer DNA segment, structure at 12.0 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qt3 | |||||||||||||||||||||||||||||||
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Title | Radiation damage study on a 16mer DNA segment, structure at 12.0 MGy dose | |||||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / radiation damage / global damage / specific damage | Function / homology | DNA / DNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å | Authors | Bugris, V. / Harmat, V. / Ferenc, G. / Brockhauser, S. / Carmichael, I. / Garman, E.F. | Funding support | Germany, Hungary, 2items |
Citation | Journal: J.Synchrotron Radiat. / Year: 2019 | 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qt3.cif.gz | 23.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qt3.ent.gz | 13.9 KB | Display | PDB format |
PDBx/mmJSON format | 6qt3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qt3_validation.pdf.gz | 373.2 KB | Display | wwPDB validaton report |
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Full document | 6qt3_full_validation.pdf.gz | 373.7 KB | Display | |
Data in XML | 6qt3_validation.xml.gz | 3.2 KB | Display | |
Data in CIF | 6qt3_validation.cif.gz | 4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/6qt3 ftp://data.pdbj.org/pub/pdb/validation_reports/qt/6qt3 | HTTPS FTP |
-Related structure data
Related structure data | 6qt1SC 6qt2C 6qt4C 6qt5C 6qt6C 6qt7 S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.26 % |
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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: 8.6-6.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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→31.36 Å / Num. obs: 3891 / % possible obs: 92.1 % / Redundancy: 2.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.041 / Rrim(I) all: 0.072 / Net I/σ(I): 5.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6QT1 Resolution: 1.8→31.36 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.73 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.174 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: 121.25 Å2 / Biso mean: 52.567 Å2 / Biso min: 30.61 Å2
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Refinement step | Cycle: final / Resolution: 1.8→31.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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