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16mer self-complementary duplex RNA with two separated native U: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 7 293 0.08 M Strontium chloride hexahydrate, 0.02 M Magnesium chloride hexahydrate, 0.04 M Sodium cacodylate trihydrate pH 7.0, 20% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride
Crystal Properties Matthews coefficient Solvent content 2.05 40.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.503 α = 90 b = 41.503 β = 90 c = 125.299 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 EIGER X 16M 2022-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033175 APS 23-ID-B
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 1.52 17.8 98.3 0.075 0.081 0.029 0.998 36.4 8.4 6587
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 1.52 1.55 99.1 0.234 0.253 0.093 0.973 3 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 1.52 17.796 6587 320 98.182 0.2 0.198 0.2045 0.2393 0.2446 21.388
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] 0.008 0.004 0.008 -0.027
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 4.636 r_lrange_it 4.62 r_angle_refined_deg 2.559 r_scangle_it 2.358 r_scangle_other 2.356 r_scbond_it 1.722 r_scbond_other 1.719 r_angle_other_deg 0.688 r_nbd_other 0.414 r_nbtor_refined 0.238
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 4.636 r_lrange_it 4.62 r_angle_refined_deg 2.559 r_scangle_it 2.358 r_scangle_other 2.356 r_scbond_it 1.722 r_scbond_other 1.719 r_angle_other_deg 0.688 r_nbd_other 0.414 r_nbtor_refined 0.238 r_chiral_restr 0.226 r_symmetry_nbd_refined 0.216 r_metal_ion_refined 0.21 r_xyhbond_nbd_refined 0.208 r_symmetry_nbd_other 0.201 r_symmetry_xyhbond_nbd_refined 0.197 r_symmetry_nbtor_other 0.086 r_nbd_refined 0.082 r_gen_planes_refined 0.028 r_bond_refined_d 0.015 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 334 Solvent Atoms 73 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling PHASER phasing