+Open data
-Basic information
Entry | Database: PDB / ID: 6cy2 | |||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | RNA octamer containing 2'-OMe, 4'Calpha-OMe U. | |||||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / oligonucleotide / modified base | Function / homology | RNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å | Authors | Harp, J.M. / Egli, M. | Citation | Journal: Nucleic Acids Res. / Year: 2018 | Title: Structural basis for the synergy of 4'- and 2'-modifications on siRNA nuclease resistance, thermal stability and RNAi activity. Authors: Harp, J.M. / Guenther, D.C. / Bisbe, A. / Perkins, L. / Matsuda, S. / Bommineni, G.R. / Zlatev, I. / Foster, D.J. / Taneja, N. / Charisse, K. / Maier, M.A. / Rajeev, K.G. / Manoharan, M. / Egli, M. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6cy2.cif.gz | 33.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6cy2.ent.gz | 23.6 KB | Display | PDB format |
PDBx/mmJSON format | 6cy2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/6cy2 ftp://data.pdbj.org/pub/pdb/validation_reports/cy/6cy2 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: RNA chain | Mass: 2649.510 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.14 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 1 mM RNA; 40 mM sodium cacodylate, 80 mM potassium chloride, 20 mM magnesium chloride, 12 mM spermine. Reservoir 40% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9183 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9183 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→21.4 Å / Num. obs: 16014 / % possible obs: 98.7 % / Redundancy: 13.5 % / CC1/2: 0.997 / Rpim(I) all: 0.03 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.4→1.45 Å / CC1/2: 0.529 / Rpim(I) all: 0.684 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.4→21.4 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0.94 / Phase error: 25.48
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 53.32 Å2 / Biso mean: 27.5932 Å2 / Biso min: 17.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→21.4 Å
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
|