+Open data
-Basic information
Entry | Database: PDB / ID: 3fa1 | ||||||||||||||||||
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Title | Crystal Structure of Tellurium Derivatized DNA | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / Tellurium DNA | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å | Authors | Sheng, J. / Tatsuya, M. / Hassan, A.E. / Huang, Z. | Citation | Journal: To be Published | Title: Crystal Structure of Tellurium Derivatized DNA Authors: Sheng, J. / Tatsuya, M. / Hassan, A.E. / Huang, Z. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fa1.cif.gz | 14.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fa1.ent.gz | 7.9 KB | Display | PDB format |
PDBx/mmJSON format | 3fa1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fa1_validation.pdf.gz | 336.5 KB | Display | wwPDB validaton report |
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Full document | 3fa1_full_validation.pdf.gz | 336.4 KB | Display | |
Data in XML | 3fa1_validation.xml.gz | 1.7 KB | Display | |
Data in CIF | 3fa1_validation.cif.gz | 1.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/3fa1 ftp://data.pdbj.org/pub/pdb/validation_reports/fa/3fa1 | HTTPS FTP |
-Related structure data
Related structure data | 1dnsS 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
#1: DNA chain | Mass: 2619.151 Da / Num. of mol.: 1 / Mutation: Tellurium modified deoxy-Uridine / Source method: obtained synthetically / Details: Tellurium contained DNA |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.61 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: MPD,sodium cacodylate,spermine tetra-HCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC Q210 / Detector: CCD / Date: Apr 12, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SAD / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→18.89 Å / Num. obs: 3659 / % possible obs: 94.4 % / Observed criterion σ(F): 50 / Observed criterion σ(I): 5 / Redundancy: 8.63 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.075 / Χ2: 0.93 / Net I/σ(I): 14.9 / Scaling rejects: 239 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Starting model: 1DNS Resolution: 1.5→18.89 Å / Occupancy max: 1 / Occupancy min: 0.35 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: THE BIJVOET PAIRS WERE USED IN PHASING
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Solvent computation | Bsol: 54.275 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 47.55 Å2 / Biso mean: 22.409 Å2 / Biso min: 14.32 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→18.89 Å
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Refine LS restraints |
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Xplor file |
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