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Yorodumi- PDB-6jjg: Crystal structure of a two-quartet DNA mixed-parallel/antiparalle... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jjg | ||||||||||||||||||||||||||||
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Title | Crystal structure of a two-quartet DNA mixed-parallel/antiparallel G-quadruplex | ||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / G-quadruplex / two-quartet / mixed-parallel/antiparallel | Function / homology | : / DNA / DNA (> 10) | Function and homology information Biological species | Pseudorabies virus Ea | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.969 Å | Authors | Zhang, Y.S. / Wei, D.G. | Funding support | China, 1items |
Citation | Journal: To Be Published | Title: Crystal structure of a two-quartet DNA mixed-parallel/antiparallel G-quadruplex Authors: Zhang, Y.S. / Parkinson, G.N. / Wagner, A. / Wei, D.G. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jjg.cif.gz | 44.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jjg.ent.gz | 31.1 KB | Display | PDB format |
PDBx/mmJSON format | 6jjg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/6jjg ftp://data.pdbj.org/pub/pdb/validation_reports/jj/6jjg | HTTPS FTP |
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-Related structure data
Related structure data | 6jjeS S: Starting model for refinement |
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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
#1: DNA chain | Mass: 4362.816 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pseudorabies virus Ea #2: Chemical | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.44 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Potassium cacodylate, Potassium chloride, Sodium cacodylate, Spermine, Potassium bromide, MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97907 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 |
Reflection | Resolution: 1.969→32.672 Å / Num. obs: 5421 / % possible obs: 97.7 % / Redundancy: 6.8 % / Rpim(I) all: 0.025 / Net I/σ(I): 15.52 |
Reflection shell | Resolution: 1.969→2.08 Å / Rpim(I) all: 0.196 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JJE Resolution: 1.969→23.075 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 31.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 166 Å2 / Biso mean: 75.888 Å2 / Biso min: 34.14 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.969→23.075 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2
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Refinement TLS params. | Method: refined / Origin x: -11.0288 Å / Origin y: -2.4043 Å / Origin z: 9.2058 Å
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Refinement TLS group |
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