+Open data
-Basic information
Entry | Database: PDB / ID: 461d | ||||||||||||||||||
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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 2 RB+ FORM CRYSTAL | Function / homology | RUBIDIUM ION / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.5 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 | 461d.cif.gz | 43.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb461d.ent.gz | 31.1 KB | Display | PDB format |
PDBx/mmJSON format | 461d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 461d_validation.pdf.gz | 371.8 KB | Display | wwPDB validaton report |
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Full document | 461d_full_validation.pdf.gz | 372 KB | Display | |
Data in XML | 461d_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | 461d_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/61/461d ftp://data.pdbj.org/pub/pdb/validation_reports/61/461d | 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 | ChemComp-RB / | #3: Chemical | #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: 2.22 Å3/Da / Density % sol: 44.69 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: SITTING DROPLETS CONTAINING 1.2 MM OLIGONUCLEOTIDE, 20 MM RB CACODYLATE PH 6.9, 6.2 MM MAGNESIUM ACETATE, 3.2 MM SPERMINE TETRACHLORIDE AGAINST RESERVOIR OF 40% MPD, VAPOR DIFFUSION, SITTING ...Details: SITTING DROPLETS CONTAINING 1.2 MM OLIGONUCLEOTIDE, 20 MM RB CACODYLATE PH 6.9, 6.2 MM MAGNESIUM ACETATE, 3.2 MM SPERMINE TETRACHLORIDE AGAINST RESERVOIR OF 40% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 295K | ||||||||||||||||||||||||||||||
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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 17, 1998 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. all: 10813 / Num. obs: 10813 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.084 |
Reflection shell | Resolution: 1.5→1.55 Å / Rmerge(I) obs: 0.094 / % possible all: 96.1 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 96.1 % |
-Processing
Software |
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Refinement | Resolution: 1.5→20 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |