+Open data
-Basic information
Entry | Database: PDB / ID: 4f4n | ||||||||||||||||||||
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Title | Crystal structure of 2-se-thymidine derivatized dna 8mer | ||||||||||||||||||||
Components | 5'-D(*Keywords | DNA / 2-SE-THYMIDINE DNA / Structural Genomics | Function / homology | DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | Authors | Zhang, W. / Sheng, J. / Huang, Z. | Citation | Journal: TO BE PUBLISHED | Title: Crystal structure of 2-se-thymidine derivatized dna 8mer Authors: Zhang, W. / Sheng, J. / Huang, Z. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f4n.cif.gz | 18.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f4n.ent.gz | 12.7 KB | Display | PDB format |
PDBx/mmJSON format | 4f4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4f4n_validation.pdf.gz | 372.3 KB | Display | wwPDB validaton report |
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Full document | 4f4n_full_validation.pdf.gz | 375.4 KB | Display | |
Data in XML | 4f4n_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 4f4n_validation.cif.gz | 5.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/4f4n ftp://data.pdbj.org/pub/pdb/validation_reports/f4/4f4n | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 2489.578 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: THE 2-SE-THYMIDINE RESIDUE WAS CHEMICALLY SYNTHESIZED AND INCORPORATED INTO DNA OLIGONUCLEOTIDE THROUGH SOLID PHASE SYNTHESIS Source: (synth.) synthetic construct (others) #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.82 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.98 Å |
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Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→18.22 Å / Num. all: 193605 / Num. obs: 10889 |
-Processing
Software | Name: REFMAC / Version: 5.5.0110 / Classification: refinement | ||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→18.22 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.949 / SU B: 0.004 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.048 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||
Displacement parameters | Biso mean: 12.491 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→18.22 Å
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LS refinement shell | Resolution: 1.302→1.335 Å / Total num. of bins used: 20
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