+Open data
-Basic information
Entry | Database: PDB / ID: 8f27 | ||||||||||||||||||||||||||||
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Title | Mirror-image DNA containing 2'-OMe-L-uridine residue | ||||||||||||||||||||||||||||
Components | Mirror-image DNA (5'-D(*Keywords | DNA / Mirror-image DNA / 2'-OMe-modification | Function / homology | DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | Authors | Zhang, W. / Dantsu, Y. | Funding support | 1items |
Citation | Journal: Chembiochem / Year: 2023 | Title: Derivatization of Mirror-Image l-Nucleic Acids with 2'-OMe Modification for Thermal and Structural Stabilization. Authors: Dantsu, Y. / Zhang, W. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f27.cif.gz | 22.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f27.ent.gz | 14.5 KB | Display | PDB format |
PDBx/mmJSON format | 8f27.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f27_validation.pdf.gz | 379.8 KB | Display | wwPDB validaton report |
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Full document | 8f27_full_validation.pdf.gz | 388.7 KB | Display | |
Data in XML | 8f27_validation.xml.gz | 4.6 KB | Display | |
Data in CIF | 8f27_validation.cif.gz | 5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/8f27 ftp://data.pdbj.org/pub/pdb/validation_reports/f2/8f27 | HTTPS FTP |
-Related structure data
Related structure data | 8f24C 7mooS S: Starting model for refinement 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
#1: DNA chain | Mass: 2442.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.67 Å3/Da / Density % sol: 53.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.5 M Lithium sulfate, 50 mM TRIS pH 8.5, 5 % w/v Glycerol |
-Data collection
Diffraction | Mean temperature: 99 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.987 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Oct 15, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→29.51 Å / Num. obs: 7021 / % possible obs: 99.4 % / Redundancy: 9.8 % / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.02 / Rrim(I) all: 0.048 / Χ2: 0.95 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 470 / CC1/2: 0.88 / Rpim(I) all: 0.402 / Rrim(I) all: 0.694 / Χ2: 0.65 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7MOO Resolution: 1.6→29.51 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.697 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.078 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.974 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→29.51 Å
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Refine LS restraints |
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