+Open data
-Basic information
Entry | Database: PDB / ID: 7kw4 | ||||||||||||||||||||
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Title | L-DNA containing 2'-fluoro modification | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / L-DNA / Fluoro modification | Function / homology | DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.03 Å | Authors | Zhang, W. / Zhang, Y. | Citation | Journal: Org.Lett. / Year: 2021 | Title: Synthesis and Structural Characterization of 2'-Deoxy-2'-fluoro-l-uridine Nucleic Acids. Authors: Dantsu, Y. / Zhang, 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 | 7kw4.cif.gz | 22.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kw4.ent.gz | 14.8 KB | Display | PDB format |
PDBx/mmJSON format | 7kw4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kw4_validation.pdf.gz | 358.1 KB | Display | wwPDB validaton report |
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Full document | 7kw4_full_validation.pdf.gz | 359 KB | Display | |
Data in XML | 7kw4_validation.xml.gz | 3.2 KB | Display | |
Data in CIF | 7kw4_validation.cif.gz | 3.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/7kw4 ftp://data.pdbj.org/pub/pdb/validation_reports/kw/7kw4 | HTTPS FTP |
-Related structure data
Related structure data | 1d79S 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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-Components
#1: DNA chain | Mass: 2414.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
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#2: Chemical | ChemComp-MG / |
#3: 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: 2.36 Å3/Da / Density % sol: 64.74 % / Description: rod-shaped crystal |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.08 M NaCl, 0.02 M MgCl2, 0.04 M Sodium Cacodylate trihydrate pH 5.5, 35% (v/v) MPD, 0.002 M hexammine cobalt(III) chloride |
-Data collection
Diffraction | Mean temperature: 99 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.03→28 Å / Num. obs: 12016 / % possible obs: 97.8 % / Redundancy: 29.4 % / Biso Wilson estimate: 9.81 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.025 / Rrim(I) all: 0.143 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.03→1.05 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.223 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 398 / CC1/2: 0.346 / Rpim(I) all: 0.562 / % possible all: 65.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1d79 Resolution: 1.03→22.497 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.64 / 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: 1.03→22.497 Å
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Refine LS restraints |
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LS refinement shell |
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