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Open data
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Basic information
Entry | Database: PDB / ID: 1qyk | ||||||||||||||||||
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Title | GCATGCT + Barium | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / Quadruplex DNA | 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 Stabilization 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 | ![]() | 27.3 KB | Display | ![]() |
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PDB format | ![]() | 18.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 344.9 KB | Display | ![]() |
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Full document | ![]() | 349.8 KB | Display | |
Data in XML | ![]() | 2.8 KB | Display | |
Data in CIF | ![]() | 3.3 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.: 2 / Source method: obtained synthetically #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.43 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: Sodium Cacodylate, Barium Chloride, Potassium Chloride, MPD, pH 5.9, 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 18, 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: 1.4→20 Å / Num. obs: 6514 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.073 |
Reflection shell | Resolution: 1.4→1.55 Å / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 4.94 / Num. unique all: 1686 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NDB entry UDG028 Resolution: 1.4→100 Å / Num. parameters: 2909 / Num. restraintsaints: 2843 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 0 / 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: 316.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→100 Å
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Refine LS restraints |
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