+Open data
-Basic information
Entry | Database: PDB / ID: 6mc3 | ||||||||||||||||||||||||||||
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Title | Crystal structure of a tetrameric DNA fold-back quadruplex | ||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / quadruplex / fold-back / hexad / non-canonical | Function / homology | DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | Authors | Chu, B. / Paukstelis, P.J. | Funding support | United States, 1items |
Citation | Journal: J. Am. Chem. Soc. / Year: 2018 | Title: Crystal Structure of a Tetrameric DNA Fold-Back Quadruplex. Authors: Chu, B. / Zhang, D. / Hwang, W. / Paukstelis, P.J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mc3.cif.gz | 58.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mc3.ent.gz | 43.3 KB | Display | PDB format |
PDBx/mmJSON format | 6mc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mc3_validation.pdf.gz | 385.4 KB | Display | wwPDB validaton report |
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Full document | 6mc3_full_validation.pdf.gz | 386.8 KB | Display | |
Data in XML | 6mc3_validation.xml.gz | 5.1 KB | Display | |
Data in CIF | 6mc3_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/6mc3 ftp://data.pdbj.org/pub/pdb/validation_reports/mc/6mc3 | HTTPS FTP |
-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: 2796.835 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-MG / #3: 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: 2.55 Å3/Da / Density % sol: 51.69 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 15% PEG400, 120 mM magnesium chloride, 30 mM sodium cacodylate, equilibrated against 20% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→28.42 Å / Num. obs: 16520 / % possible obs: 99.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.036 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.57→1.6 Å / Rmerge(I) obs: 3.668 / Num. unique obs: 802 / Rpim(I) all: 1.531 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→28.42 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.968 / SU B: 10.313 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.094 / 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: 37.605 Å2
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Refinement step | Cycle: 1 / Resolution: 1.57→28.42 Å
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Refine LS restraints |
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