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Open data
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Basic information
Entry | Database: PDB / ID: 6cy2 | |||||||||||||||||||||||
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Title | RNA octamer containing 2'-OMe, 4'Calpha-OMe U. | |||||||||||||||||||||||
![]() | RNA (5'-R(*![]() RNA / oligonucleotide / modified base | Function / homology | RNA | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Harp, J.M. / Egli, M. | ![]() ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 33.7 KB | Display | ![]() |
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PDB format | ![]() | 23.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 387 KB | Display | ![]() |
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Full document | ![]() | 390.1 KB | Display | |
Data in XML | ![]() | 4.2 KB | Display | |
Data in CIF | ![]() | 5.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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 / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.14 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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