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Structure of dsRNA 16mer containing 4'-C-methyladenosine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 294 10% MPD, 40 mM Sodium cacodylate trihydrate pH 6.0 12 mM Spermine, 80 mM KCl
Crystal Properties Matthews coefficient Solvent content 2.17 43.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.038 α = 90 b = 43.038 β = 90 c = 127.318 γ = 120
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 DECTRIS EIGER2 XE 16M 2024-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.91943 SSRL BL12-1
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 37.3 99.7 0.09 0.094 0.029 0.999 11.5 10.3 24409 -3
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 98.7 1.225 1.32 0.482 0.264 1.6 7.3
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 SAD FREE R-VALUE 1.801 37.3 24365 1252 99.73 0.214 0.2122 0.2257 0.2459 0.254 39.27
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] 0.694 0.347 0.694 -2.251
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.212 r_lrange_other 5.199 r_scangle_it 3.572 r_scangle_other 3.571 r_scbond_other 2.725 r_scbond_it 2.724 r_angle_refined_deg 1.803 r_angle_other_deg 0.524 r_nbtor_refined 0.264 r_symmetry_nbd_other 0.197
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.212 r_lrange_other 5.199 r_scangle_it 3.572 r_scangle_other 3.571 r_scbond_other 2.725 r_scbond_it 2.724 r_angle_refined_deg 1.803 r_angle_other_deg 0.524 r_nbtor_refined 0.264 r_symmetry_nbd_other 0.197 r_xyhbond_nbd_refined 0.195 r_nbd_other 0.188 r_symmetry_xyhbond_nbd_refined 0.157 r_nbd_refined 0.135 r_dihedral_angle_other_2_deg 0.134 r_symmetry_nbd_refined 0.091 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.063 r_chiral_restr_other 0.061 r_gen_planes_refined 0.013 r_bond_refined_d 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2034 Solvent Atoms 101 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PDB_EXTRACT data extraction AutoSol phasing