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Yorodumi- PDB-4l26: Crystal structure of DNA duplex containing consecutive T-T mispai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l26 | ||||||||||||||||||
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Title | Crystal structure of DNA duplex containing consecutive T-T mispairs (Br-derivative) | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / T-T mispair / A-T-T triplet / non-helical DNA duplex | Function / homology | DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å | Authors | Kondo, J. / Yamada, T. / Hirose, C. / Tanaka, Y. / Ono, A. | Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 | Title: Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson-Crick-like T-Hg(II) -T Base Pairs Authors: Kondo, J. / Yamada, T. / Hirose, C. / Okamoto, I. / Tanaka, Y. / Ono, A. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l26.cif.gz | 25 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l26.ent.gz | 16.3 KB | Display | PDB format |
PDBx/mmJSON format | 4l26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4l26_validation.pdf.gz | 371.7 KB | Display | wwPDB validaton report |
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Full document | 4l26_full_validation.pdf.gz | 371.7 KB | Display | |
Data in XML | 4l26_validation.xml.gz | 4.6 KB | Display | |
Data in CIF | 4l26_validation.cif.gz | 6.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/4l26 ftp://data.pdbj.org/pub/pdb/validation_reports/l2/4l26 | 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: 3733.274 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized #2: 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: 2.16 Å3/Da / Density % sol: 43.17 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Sodium Cacodylate, Spermine tetrahydrochloride, 2-methyl-2,4-pentanediol, ammonium chloride , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 277 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1.0, 0.91942, 0.92006 | ||||||||||||
Detector | Date: Oct 22, 2012 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.4→21.94 Å / Num. obs: 12212 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.4→21.94 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0
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Solvent computation | Bsol: 52.9486 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 52.41 Å2 / Biso mean: 19.0444 Å2 / Biso min: 9.74 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→21.94 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Xplor file |
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