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Open data
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Basic information
Entry | Database: PDB / ID: 460d | ||||||||||||||||||
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Title | A "HYDRAT-ION SPINE" IN A B-DNA MINOR GROOVE | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / B-DNA / DODECAMER DUPLEX / TYPE 1 RB+ FORM CRYSTAL | Function / homology | RUBIDIUM ION / DNA / DNA (> 10) | ![]() Method | ![]() ![]() ![]() Tereshko, V. / Minasov, G. / Egli, M. | ![]() Journal: J.Am.Chem.Soc. / Year: 1999 | Title: A "Hydrat-Ion Spine" in a B-DNA minor groove Authors: Tereshko, V. / Minasov, G. / Egli, M. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44.4 KB | Display | ![]() |
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PDB format | ![]() | 31.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 377.8 KB | Display | ![]() |
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Full document | ![]() | 377.6 KB | Display | |
Data in XML | ![]() | 5.9 KB | Display | |
Data in CIF | ![]() | 8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 3681.383 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | #3: Chemical | ChemComp-RB / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.84 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 275 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: SITTING DROPLETS CONTAINING 1.2 MM OLIGONUCLEOTIDE, 20 MM RB CACODYLATE PH 6.9, 25 MM MAGNESIUM ACETATE, 3.2 MM SPERMINE TETRACLORIDE AGAINST RESERVOIR OF 40% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 275K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 13, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.10012 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→20 Å / Num. all: 20661 / Num. obs: 20661 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.068 |
Reflection shell | Resolution: 1.2→1.24 Å / Rmerge(I) obs: 0.115 / % possible all: 93.3 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 93.3 % |
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Processing
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Refinement | Resolution: 1.2→20 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-96 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |