+Open data
-Basic information
Entry | Database: PDB / ID: 6ip3 | ||||||||||||||||||||||||||||
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Title | Structure of human telomeric DNA at 1.4 Angstroms resolution | ||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / Human telomere / parallel G-quadruplex | Function / homology | : / DNA / DNA (> 10) | Function and homology information Biological species | Homo sapiens (human) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | Authors | Saikrishnan, K. / Nuthanakanti, A. / Srivatsan, S.G. / Ahmad, I. | Funding support | India, 1items |
Citation | Journal: Nucleic Acids Res. / Year: 2019 | Title: Probing G-quadruplex topologies and recognition concurrently in real time and 3D using a dual-app nucleoside probe. Authors: Nuthanakanti, A. / Ahmed, I. / Khatik, S.Y. / Saikrishnan, K. / Srivatsan, S.G. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ip3.cif.gz | 50.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ip3.ent.gz | 37 KB | Display | PDB format |
PDBx/mmJSON format | 6ip3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/6ip3 ftp://data.pdbj.org/pub/pdb/validation_reports/ip/6ip3 | HTTPS FTP |
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-Related structure data
Related structure data | 6ip7C 6iswC 1kf1S 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: 6983.497 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||
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#2: Chemical | #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: 2.83 Å3/Da / Density % sol: 56.57 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.05M sodium cacodylate (pH = 7.2), 0.4M ammonium sulfate, 0.05M KCl, 0.01M CaCl2, 15% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. obs: 15493 / % possible obs: 100 % / Redundancy: 16.3 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.4→1.42 Å / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 777 / Rsym value: 0.88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KF1 Resolution: 1.4→28.42 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 19.65
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→28.42 Å
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Refine LS restraints |
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LS refinement shell |
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