+Open data
-Basic information
Entry | Database: PDB / ID: 3tok | ||||||
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Title | Assaying the energies of biological halogen bonds. | ||||||
Components |
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Keywords | DNA / DNA Holliday Junction | ||||||
Function / homology | DNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Carter, M. / Ho, P.S. | ||||||
Citation | Journal: CRYST.GROWTH DES. / Year: 2011 Title: Assaying the Energies of Biological Halogen Bonds Authors: Carter, M. / Ho, P.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tok.cif.gz | 31.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tok.ent.gz | 23.2 KB | Display | PDB format |
PDBx/mmJSON format | 3tok.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/3tok ftp://data.pdbj.org/pub/pdb/validation_reports/to/3tok | HTTPS FTP |
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-Related structure data
Related structure data | 2orgS S: Starting model for refinement |
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Similar structure data |
-Links
-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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Details | The asymmetric unit contains two DNA strands. The biological unit is deposited as four strands, containing two pairs of symmetry related alternative conformations |
-Components
#1: DNA chain | Mass: 3029.994 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic construct |
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#2: DNA chain | Mass: 3061.003 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic construct |
#3: Chemical | ChemComp-NA / |
#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: 2.31 Å3/Da / Density % sol: 46.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 25mM Sodium Calcodylate, 10mM Calcuim Chloride, 1.1mM Spermine, and 0.35mM of each DNA strand, pH 7.0, vapor diffusion, sitting drop,temperature 298K, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Jun 24, 2009 |
Radiation | Monochromator: Rosenbaum-rock SI(111) sagitally focused monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→40 Å / Num. obs: 10026 / % possible obs: 97.98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ORG Resolution: 1.74→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.74→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.84 Å |