+Open data
-Basic information
Entry | Database: PDB / ID: 460d | ||||||||||||||||||
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Title | A "HYDRAT-ION SPINE" IN A B-DNA MINOR GROOVE | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DODECAMER DUPLEX / TYPE 1 RB+ FORM CRYSTAL | Function / homology | RUBIDIUM ION / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å | Authors | Tereshko, V. / Minasov, G. / Egli, M. | Citation | 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 460d.cif.gz | 44.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb460d.ent.gz | 31.7 KB | Display | PDB format |
PDBx/mmJSON format | 460d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 460d_validation.pdf.gz | 377.8 KB | Display | wwPDB validaton report |
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Full document | 460d_full_validation.pdf.gz | 377.6 KB | Display | |
Data in XML | 460d_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 460d_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/60/460d ftp://data.pdbj.org/pub/pdb/validation_reports/60/460d | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1.10012 |
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 % |
-Processing
Software |
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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 |