+Open data
-Basic information
Entry | Database: PDB / ID: 8i50 | |||||||||||||||||||||||||||||||||||||||||||||||||
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Title | Crystal structure of DNA octamer containing GuNA[Me,Me] | |||||||||||||||||||||||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / OLIGONUCLEOTIDE / MODIFIED BASE | Function / homology | DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.95 Å | Authors | Aoyama, H. / Obika, S. / Yamaguchi, T. | Funding support | Japan, 8items |
Citation | Journal: Nucleic Acids Res. / Year: 2023 | Title: Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids. Authors: Yamaguchi, T. / Horie, N. / Aoyama, H. / Kumagai, S. / Obika, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i50.cif.gz | 25.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i50.ent.gz | 15.4 KB | Display | PDB format |
PDBx/mmJSON format | 8i50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i50_validation.pdf.gz | 371 KB | Display | wwPDB validaton report |
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Full document | 8i50_full_validation.pdf.gz | 371.9 KB | Display | |
Data in XML | 8i50_validation.xml.gz | 3.3 KB | Display | |
Data in CIF | 8i50_validation.cif.gz | 4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/8i50 ftp://data.pdbj.org/pub/pdb/validation_reports/i5/8i50 | HTTPS FTP |
-Related structure data
Related structure data | 8hisC 8hu5C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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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-Components
#1: DNA chain | Mass: 2588.606 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.63 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 10% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.040M Sodium cacodylate trihydrate pH 7.0, 0.012M Spermine tetrahydrochloride, 0.080M Potassium chloride, 0.020M Magnesium chloride hexahydrate PH range: 7 |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9199 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9199 Å / Relative weight: 1 |
Reflection | Resolution: 0.95→40.34 Å / Num. obs: 16392 / % possible obs: 99.5 % / Redundancy: 18.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.014 / Χ2: 1.01 / Net I/σ(I): 34.6 |
Reflection shell | Resolution: 0.95→0.97 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1.255 / Mean I/σ(I) obs: 1.6 / Num. measured obs: 5846 / Num. unique obs: 720 / CC1/2: 0.646 / Rpim(I) all: 0.458 / Rrim(I) all: 0.78 / Χ2: 0.95 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 0.95→26.4 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0.17 / Phase error: 17.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.95→26.4 Å
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Refine LS restraints |
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LS refinement shell |
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