+Open data
-Basic information
Entry | Database: PDB / ID: 3q61 | ||||||||||||||||||
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Title | 3'-Fluoro Hexitol Nucleic Acid DNA Structure | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / A-FORM DNA / 3'-Fluoro Hexitol Nucleic Acid / FHNA / Antisense oligonucleotides | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å | Authors | Seth, P.R. / Allerson, C.R. / Prakash, T.P. / Siwkowski, A. / Berdeja, A. / Yu, J. / Pallan, P.S. / Watt, A.T. / Gaus, H. / Bhat, B. ...Seth, P.R. / Allerson, C.R. / Prakash, T.P. / Siwkowski, A. / Berdeja, A. / Yu, J. / Pallan, P.S. / Watt, A.T. / Gaus, H. / Bhat, B. / Egli, M. / Swayze, E.E. | Citation | Journal: J.Am.Chem.Soc. / Year: 2011 | Title: Synthesis, improved antisense activity and structural rationale for the divergent RNA affinities of 3'-fluoro hexitol nucleic acid (FHNA and Ara-FHNA) modified oligonucleotides. Authors: Egli, M. / Pallan, P.S. / Allerson, C.R. / Prakash, T.P. / Berdeja, A. / Yu, J. / Lee, S. / Watt, A. / Gaus, H. / Bhat, B. / Swayze, E.E. / Seth, P.P. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q61.cif.gz | 34.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q61.ent.gz | 24.3 KB | Display | PDB format |
PDBx/mmJSON format | 3q61.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3q61_validation.pdf.gz | 382.4 KB | Display | wwPDB validaton report |
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Full document | 3q61_full_validation.pdf.gz | 386.4 KB | Display | |
Data in XML | 3q61_validation.xml.gz | 4.5 KB | Display | |
Data in CIF | 3q61_validation.cif.gz | 5.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/3q61 ftp://data.pdbj.org/pub/pdb/validation_reports/q6/3q61 | HTTPS FTP |
-Related structure data
Related structure data | 3ey2S 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: 3077.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized oligonucleotide #2: Water | ChemComp-HOH / | |
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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: 2.23 Å3/Da / Density % sol: 44.94 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20 mM sodium cacodylate, 6 mM sodium chloride, 40 mM potassium chloride, 6 mM spermine tetrahydrochloride, 5% v/v MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 12, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→31.31 Å / Num. all: 7883 / Num. obs: 7849 / % possible obs: 99.56 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 40.5 |
Reflection shell | Resolution: 1.56→1.62 Å / Redundancy: 7 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 11.3 / Num. unique all: 791 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EY2 Resolution: 1.56→31.31 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.745 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 17.373 Å2
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Refinement step | Cycle: LAST / Resolution: 1.56→31.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.56→1.6 Å / Total num. of bins used: 20
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