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16mer self-complementary duplex RNA with dI:s(2)C pair sequence 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9MDY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2 M Calcium chloride dihydrate, 0.05 M HEPES sodium pH 7.5, 28% v/v Polyethylene glycol 400, 0.002 M Spermine
Crystal Properties Matthews coefficient Solvent content 1.98 37.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.898 α = 90 b = 40.898 β = 90 c = 124.979 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 99 PIXEL DECTRIS EIGER X 16M 2025-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97933 NSLS-II 17-ID-2
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 1.243 34.077 100 0.128 0.135 0.044 0.997 12.5 17.6 11727
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 1.243 1.265 100 2 2.14 0.754 0.439 2 14.7
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 1.243 34.077 11724 1173 99.957 0.191 0.1864 0.1931 0.229 0.2302 12.619
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] 0.002 0.001 0.002 -0.007
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 4.617 r_lrange_other 4.035 r_angle_refined_deg 2.079 r_scangle_it 1.802 r_scangle_other 1.801 r_scbond_it 1.256 r_scbond_other 1.254 r_angle_other_deg 0.768 r_xyhbond_nbd_refined 0.294 r_nbtor_refined 0.239
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 4.617 r_lrange_other 4.035 r_angle_refined_deg 2.079 r_scangle_it 1.802 r_scangle_other 1.801 r_scbond_it 1.256 r_scbond_other 1.254 r_angle_other_deg 0.768 r_xyhbond_nbd_refined 0.294 r_nbtor_refined 0.239 r_symmetry_nbd_other 0.205 r_metal_ion_refined 0.199 r_symmetry_xyhbond_nbd_refined 0.185 r_nbd_other 0.147 r_symmetry_nbd_refined 0.097 r_nbd_refined 0.086 r_chiral_restr 0.076 r_symmetry_nbtor_other 0.075 r_dihedral_angle_other_2_deg 0.05 r_gen_planes_refined 0.029 r_bond_refined_d 0.012 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 334 Solvent Atoms 80 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing