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16mer self-complementary duplex RNA with two separated s(2)U:s(2)U pairs
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ND4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.075 M Sodium chloride, 0.002 M Calcium chloride dihydrate, 0.05 M Sodium cacodylate trihydrate pH 6.0, 30% w/v 1,6 Hexanediol, 0.0005 M Spermine
Crystal Properties Matthews coefficient Solvent content 2 38.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.261 α = 90 b = 41.261 β = 90 c = 124.239 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 PILATUS3 6M 2022-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 2.0.1 1.037690 ALS 2.0.1
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 1.5 31 100 0.077 0.082 0.029 0.998 14.2 8.7 6853
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 1.5 1.53 100 0.235 0.249 0.081 0.973 2.3 9
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 1.5 30.993 6848 328 99.883 0.179 0.1774 0.1818 0.2103 0.2152 18.188
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] -0.009 -0.004 -0.009 0.028
RMS Deviations Key Refinement Restraint Deviation r_angle_other_deg 3.968 r_lrange_other 3.312 r_lrange_it 3.297 r_angle_refined_deg 2.577 r_chiral_restr_other 2.519 r_scangle_it 2.012 r_scangle_other 2.01 r_scbond_it 1.552 r_scbond_other 1.55 r_nbd_other 0.382
RMS Deviations Key Refinement Restraint Deviation r_angle_other_deg 3.968 r_lrange_other 3.312 r_lrange_it 3.297 r_angle_refined_deg 2.577 r_chiral_restr_other 2.519 r_scangle_it 2.012 r_scangle_other 2.01 r_scbond_it 1.552 r_scbond_other 1.55 r_nbd_other 0.382 r_nbtor_refined 0.238 r_symmetry_nbd_other 0.207 r_symmetry_nbd_refined 0.202 r_chiral_restr 0.196 r_nbd_refined 0.109 r_symmetry_xyhbond_nbd_refined 0.108 r_xyhbond_nbd_refined 0.103 r_symmetry_nbtor_other 0.092 r_bond_other_d 0.044 r_gen_planes_refined 0.026 r_bond_refined_d 0.021 r_metal_ion_refined 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 334 Solvent Atoms 54 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing