+Open data
-Basic information
Entry | Database: PDB / ID: 1qyl | ||||||||||||||||||
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Title | GCATGCT + Vanadium | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / Quadruplex DNA | Function / homology | VANADIUM ION / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1 Å | Authors | Cardin, C.J. / Gan, Y. / Thorpe, J.H. / Teixeira, S.C.M. / Gale, B.C. / Moraes, M.I.A. | Citation | Journal: To be Published | Title: Metal Ion Distribution and Stabilisation of the DNA Quadruplex Structure Formed by d(GCATGCT) Authors: Cardin, C.J. / GAN, Y. / Thorpe, J.H. / Teixeira, S.C.M. / Gale, B.C. / Moraes, M.I.A. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qyl.cif.gz | 19.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qyl.ent.gz | 11.9 KB | Display | PDB format |
PDBx/mmJSON format | 1qyl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qyl_validation.pdf.gz | 355.2 KB | Display | wwPDB validaton report |
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Full document | 1qyl_full_validation.pdf.gz | 357.6 KB | Display | |
Data in XML | 1qyl_validation.xml.gz | 3.3 KB | Display | |
Data in CIF | 1qyl_validation.cif.gz | 4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/1qyl ftp://data.pdbj.org/pub/pdb/validation_reports/qy/1qyl | 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: 2113.410 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Chemical | ChemComp-V / |
#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: 1.81 Å3/Da / Density % sol: 32.16 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.7 Details: NaCacodylate, Vanadium Chloride, Sodium Chloride, MPD, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8416 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 19, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8416 Å / Relative weight: 1 |
Reflection | Resolution: 1→5.8 Å / Num. obs: 8848 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.095 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1→1.2 Å / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 12.63 / Num. unique all: 3718 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: NDB entry udg028 Resolution: 1→5.8 Å / Num. parameters: 1655 / Num. restraintsaints: 1425 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 180.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→5.8 Å
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Refine LS restraints |
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