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Open data
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Basic information
Entry | Database: PDB / ID: 1qzl | ||||||||||||||||||
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Title | GCATGCT + Cobalt | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / DNA quadruplex | Function / homology | : / DNA | ![]() Method | ![]() ![]() ![]() ![]() Cardin, C.J. / Gan, Y. / Thorpe, J.H. / Teixeira, S.C.M. / Gale, B.C. / Moraes, M.I.A. | ![]() ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 12.1 KB | Display | ![]() |
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PDB format | ![]() | 7.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 381.5 KB | Display | ![]() |
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Full document | ![]() | 383.4 KB | Display | |
Data in XML | ![]() | 2.7 KB | Display | |
Data in CIF | ![]() | 2.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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-CO / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.74 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: sodium cacodylate, Cobalt dichloride, potassium chloride, MPD, pH 6.5, 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: ![]() ![]() ![]() |
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: 2.85→30.606 Å / Num. obs: 522 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 41.857 Å2 / Rmerge(I) obs: 0.1573 / Rsym value: 0.1507 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 2.85→3 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 2.1 / Num. unique all: 69 / Rsym value: 0.288 / % possible all: 99.5 |
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Processing
Software |
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Refinement | Method to determine structure: ![]()
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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: 37.898 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→30.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→2.924 Å / Total num. of bins used: 20 /
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