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16mer self-complementary duplex RNA with s(2)C:G 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 7.5 293 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES sodium pH 7.5, 30% v/v Polyethylene glycol 400
Crystal Properties Matthews coefficient Solvent content 1.98 37.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.217 α = 90 b = 41.217 β = 90 c = 123.468 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 2024-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.000050 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 1.6 50 97.5 0.106 0.115 0.044 0.937 14.8 7.7 5469
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 1.6 1.63 82.9 0.254 0.293 0.141 0.967 2.7 3.3
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 MOLECULAR REPLACEMENT THROUGHOUT 1.6 34.291 5162 253 91.785 0.179 0.1756 0.1819 0.2641 0.2646 13.518
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 0.001 -0.002
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 7.856 r_lrange_other 7.351 r_angle_refined_deg 2.261 r_scangle_it 1.956 r_scangle_other 1.954 r_scbond_it 1.372 r_scbond_other 1.371 r_angle_other_deg 0.742 r_xyhbond_nbd_refined 0.264 r_nbtor_refined 0.242
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 7.856 r_lrange_other 7.351 r_angle_refined_deg 2.261 r_scangle_it 1.956 r_scangle_other 1.954 r_scbond_it 1.372 r_scbond_other 1.371 r_angle_other_deg 0.742 r_xyhbond_nbd_refined 0.264 r_nbtor_refined 0.242 r_symmetry_xyhbond_nbd_refined 0.219 r_dihedral_angle_other_2_deg 0.217 r_symmetry_nbd_other 0.2 r_nbd_other 0.155 r_nbd_refined 0.093 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.082 r_symmetry_nbd_refined 0.078 r_gen_planes_refined 0.022 r_bond_refined_d 0.011 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 336 Solvent Atoms 103 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing