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1.80 A crystal structure of RNA/2'-O-methyl-RNA heteroduplex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OW0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 1 mM duplex, 1.4 M Li2SO4, 50 mM sodium cacodylate, 1 mM spermine
Crystal Properties Matthews coefficient Solvent content 2.28 46.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.103 α = 90 b = 49.303 β = 97.149 c = 55.868 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL RIGAKU HyPix-6000HE 2021-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU PhotonJet-S 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.8 19.011 99.7 0.081 0.094 0.046 0.998 11.7 4.2 15124 8.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 100 0.636 0.747 0.382 0.817 2.1 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 19.011 15077 723 99.413 0.191 0.188 0.199 0.2561 0.2659 26.582
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -1.766 0.125 -0.416 2.085
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 6.353 r_lrange_other 5.963 r_scangle_it 3.569 r_scangle_other 3.522 r_scbond_it 2.429 r_scbond_other 2.399 r_angle_refined_deg 1.952 r_angle_other_deg 0.502 r_nbtor_refined 0.24 r_symmetry_nbd_refined 0.223
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 6.353 r_lrange_other 5.963 r_scangle_it 3.569 r_scangle_other 3.522 r_scbond_it 2.429 r_scbond_other 2.399 r_angle_refined_deg 1.952 r_angle_other_deg 0.502 r_nbtor_refined 0.24 r_symmetry_nbd_refined 0.223 r_xyhbond_nbd_refined 0.198 r_symmetry_nbd_other 0.195 r_dihedral_angle_other_2_deg 0.189 r_nbd_other 0.178 r_symmetry_xyhbond_nbd_refined 0.144 r_nbd_refined 0.117 r_symmetry_nbtor_other 0.105 r_chiral_restr 0.09 r_gen_planes_refined 0.015 r_bond_refined_d 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1158 Solvent Atoms 316 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing