+Open data
-Basic information
Entry | Database: PDB / ID: 1r2o | ||||||||||||||||||
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Title | d(GCATGCT) + Ni2+ | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / METAL ION / DNA QUADRUPLEX | Function / homology | NICKEL (II) ION / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | Authors | Cardin, J.C. / 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 Stabilization of the DNA Quadruplex Structure Formed by d(GCATGCT) Authors: Cardin, J.C. / 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 | 1r2o.cif.gz | 13 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r2o.ent.gz | 8.4 KB | Display | PDB format |
PDBx/mmJSON format | 1r2o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r2o_validation.pdf.gz | 381.8 KB | Display | wwPDB validaton report |
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Full document | 1r2o_full_validation.pdf.gz | 381.6 KB | Display | |
Data in XML | 1r2o_validation.xml.gz | 2.5 KB | Display | |
Data in CIF | 1r2o_validation.cif.gz | 2.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/1r2o ftp://data.pdbj.org/pub/pdb/validation_reports/r2/1r2o | 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-NI / |
#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: 1.86 Å3/Da / Density % sol: 34.03 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.7 Details: sodium cacodylate, nickel dichloride, potassium 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: X11 / Wavelength: 0.8126 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8126 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→30.71 Å / Num. obs: 857 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.47 % / Biso Wilson estimate: 31.357 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.38→2.51 Å / Redundancy: 17.1 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 4 / Num. unique all: 119 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→30.71 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.897 / SU B: 4.499 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.661 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.848 Å2
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Refinement step | Cycle: LAST / Resolution: 2.38→30.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.38→2.445 Å / Total num. of bins used: 20 /
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