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16mer self-complementary duplex RNA with s(2)C:I pair sequence 2
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 293 2.0 M Ammonium sulfate, 5% v/v 2-Propanol
Crystal Properties Matthews coefficient Solvent content 1.96 37.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.942 α = 90 b = 40.942 β = 90 c = 123.477 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 EIGER2 S 9M 2024-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.000026 ALS 8.2.1
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 1.33 50 98.4 0.068 0.072 0.026 0.978 21.6 7.8 9369 13.46
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 1.33 1.35 92 0.471 0.546 0.267 0.85 2.5 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 FREE R-VALUE 1.33 30.747 9192 451 96.504 0.19 0.188 0.1929 0.2185 0.2223 12.883
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] -0.001
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.286 r_lrange_other 5.148 r_angle_refined_deg 2.348 r_scangle_it 1.937 r_scangle_other 1.935 r_scbond_it 1.396 r_scbond_other 1.395 r_angle_other_deg 0.901 r_xyhbond_nbd_refined 0.241 r_nbtor_refined 0.24
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.286 r_lrange_other 5.148 r_angle_refined_deg 2.348 r_scangle_it 1.937 r_scangle_other 1.935 r_scbond_it 1.396 r_scbond_other 1.395 r_angle_other_deg 0.901 r_xyhbond_nbd_refined 0.241 r_nbtor_refined 0.24 r_symmetry_nbd_other 0.206 r_nbd_other 0.155 r_symmetry_xyhbond_nbd_refined 0.145 r_symmetry_nbd_refined 0.109 r_chiral_restr 0.096 r_nbd_refined 0.088 r_dihedral_angle_other_2_deg 0.08 r_symmetry_nbtor_other 0.08 r_gen_planes_refined 0.029 r_bond_refined_d 0.017 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 335 Solvent Atoms 84 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing