+Open data
-Basic information
Entry | Database: PDB / ID: 5der | ||||||
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Title | RNA oligonucleotide containing (R)-C5'-ME-2'F U | ||||||
Components | RNA oligonucleotide containing (R)-C5'-Me-2'-FU | ||||||
Keywords | RNA / oligonucleotide | ||||||
Function / homology | RNA Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Harp, J.M. / Egli, M. | ||||||
Citation | Journal: J.Org.Chem. / Year: 2016 Title: Structural Basis of Duplex Thermodynamic Stability and Enhanced Nuclease Resistance of 5'-C-Methyl Pyrimidine-Modified Oligonucleotides. Authors: Kel In, A.V. / Zlatev, I. / Harp, J. / Jayaraman, M. / Bisbe, A. / O Shea, J. / Taneja, N. / Manoharan, R.M. / Khan, S. / Charisse, K. / Maier, M.A. / Egli, M. / Rajeev, K.G. / Manoharan, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5der.cif.gz | 38.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5der.ent.gz | 22.3 KB | Display | PDB format |
PDBx/mmJSON format | 5der.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/5der ftp://data.pdbj.org/pub/pdb/validation_reports/de/5der | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: RNA chain | Mass: 2542.579 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #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: 2.08 Å3/Da / Density % sol: 40.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 40 mM sodium cacodylate, 20 mM hexamine Co(III) chloride, 12 mM NaCl, 80 mM KCl, reservoir 40% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54178 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Sep 30, 2014 / Details: Montel multilayer, confocal mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25.34 Å / Num. obs: 15381 / % possible obs: 99.6 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.57 |
Reflection shell | Resolution: 1.8→1.89 Å / Redundancy: 2.73 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 1.77 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Resolution: 1.8→25.34 Å / Cross valid method: FREE R-VALUE / σ(F): 0.143 / Phase error: 31.818088423
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.4012714523 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→25.34 Å
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Refine LS restraints |
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LS refinement shell |
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