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Open data
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Basic information
Entry | Database: PDB / ID: 3ggi | ||||||||||||||||||
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Title | Locating monovalent cations in one turn of G/C rich B-DNA | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / CATIONS / DIVALENT CATIONS / MONOVALENT CATIONS / THALLIUM ION | Function / homology | THALLIUM (I) ION / DNA | ![]() Method | ![]() ![]() ![]() ![]() Maehigashi, T. / Moulaei, T. / Watkins, D. / Komeda, S. / Williams, L.D. | ![]() ![]() Title: Locating monovalent cations in one turn of G/C rich B-DNA Authors: Maehigashi, T. / Moulaei, T. / Watkins, D. / Komeda, S. / Williams, L.D. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 34.5 KB | Display | ![]() |
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PDB format | ![]() | 23.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 366.5 KB | Display | ![]() |
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Full document | ![]() | 366.6 KB | Display | |
Data in XML | ![]() | 4.6 KB | Display | |
Data in CIF | ![]() | 6.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ggkC ![]() 1bd1S C: citing same article ( S: Starting model for refinement |
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Similar 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: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic construct | ||||
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#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-TL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.83 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MPD, Magnesium acetate, Thallium acetate, Cacodylic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 21, 2004 |
Radiation | Monochromator: Cryogenically cooled Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97582 Å / Relative weight: 1 |
Reflection | Resolution: 0.92→30.6 Å / Num. obs: 13522 / % possible obs: 76 % / Redundancy: 7 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 61 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: DNA coordinates from PDB Entry 1bd1 (Heinemann and Alings) Resolution: 0.98→15.31 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.449 / SU ML: 0.012 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.029 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.856 Å2
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Refinement step | Cycle: LAST / Resolution: 0.98→15.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.978→1.003 Å / Total num. of bins used: 20
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