+Open data
-Basic information
Entry | Database: PDB / ID: 2hto | ||||||
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Title | Ruthenium hexammine ion interactions with Z-DNA | ||||||
Components |
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Keywords | DNA / Z-DNA / DOUBLE HELIX | ||||||
Function / homology | RUTHENIUM (III) HEXAAMINE ION / DNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | ||||||
Authors | Bharanidharan, D. / Thiyagarajan, S. / Gautham, N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: Hexammineruthenium(III) ion interactions with Z-DNA Authors: Bharanidharan, D. / Thiyagarajan, S. / Gautham, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hto.cif.gz | 18.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hto.ent.gz | 11.2 KB | Display | PDB format |
PDBx/mmJSON format | 2hto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hto_validation.pdf.gz | 388 KB | Display | wwPDB validaton report |
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Full document | 2hto_full_validation.pdf.gz | 394.9 KB | Display | |
Data in XML | 2hto_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | 2hto_validation.cif.gz | 5.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/2hto ftp://data.pdbj.org/pub/pdb/validation_reports/ht/2hto | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 1794.206 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 1825.216 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Chemical | ChemComp-NRU / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.704421 Å3/Da / Density % sol: 51.73 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: MPD, sodium cacodylate, ruthenium hexammine chloride, spermine, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 16, 2004 |
Radiation | Monochromator: NIL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→30 Å / Num. all: 3590 / Num. obs: 3590 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.04 % / Rmerge(I) obs: 0.0526 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 1.54→1.6 Å / Redundancy: 4.84 % / Rmerge(I) obs: 0.3578 / Mean I/σ(I) obs: 1.8 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NDB ENTRY ZD0013 Resolution: 1.54→25.35 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.085 / SU ML: 0.072 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.109 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.782 Å2
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Refinement step | Cycle: LAST / Resolution: 1.54→25.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.546→1.586 Å / Total num. of bins used: 20
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