+Open data
-Basic information
Entry | Database: PDB / ID: 6rou | |||||||||
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Title | REP related 18-mer DNA | |||||||||
Components | REP related 18-mer DNA from H. parasuis | |||||||||
Keywords | DNA / A-DNA / Duplex / non-canonical pairing / T-T mismatch / REP / Haemophilus parasuis | |||||||||
Function / homology | STRONTIUM ION / DNA / DNA (> 10) Function and homology information | |||||||||
Biological species | Glaesserella parasuis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.902 Å | |||||||||
Authors | Kolenko, P. / Svoboda, J. / Schneider, B. | |||||||||
Funding support | Czech Republic, 2items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2020 Title: Structural variability of CG-rich DNA 18-mers accommodating double T-T mismatches. Authors: Kolenko, P. / Svoboda, J. / Cerny, J. / Charnavets, T. / Schneider, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rou.cif.gz | 21.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rou.ent.gz | 12 KB | Display | PDB format |
PDBx/mmJSON format | 6rou.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ro/6rou ftp://data.pdbj.org/pub/pdb/validation_reports/ro/6rou | HTTPS FTP |
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-Related 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: 5508.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Glaesserella parasuis (bacteria) |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.96 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Natrix crystallization screen (Hampton Research) precipitant 30-32% (+/-)-2-Methyl-2,4-pentanediol buffer 0.04M Sodium cacodylate trihydrate salt 0.04 M Lithium chloride 0.08 M Strontium ...Details: Natrix crystallization screen (Hampton Research) precipitant 30-32% (+/-)-2-Methyl-2,4-pentanediol buffer 0.04M Sodium cacodylate trihydrate salt 0.04 M Lithium chloride 0.08 M Strontium chloride hexahydrate additive 0.012 M spermine tetrahydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.979491 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 8, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979491 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→44.97 Å / Num. obs: 1758 / % possible obs: 99.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 116 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.019 / Rrim(I) all: 0.064 / Χ2: 0.98 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.9→3.1 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 299 / CC1/2: 0.958 / Rpim(I) all: 0.188 / Rrim(I) all: 0.735 / Χ2: 0.88 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Deposition ID D_1200013700 Resolution: 2.902→35.442 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.46
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 122 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.902→35.442 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 2.9 Å |