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16mer self-complementary duplex RNA with dA:U 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 5.5 293 0.08 M Sodium chloride, 0.02 M Magnesium chloride hexahydrate, 0.04 M Sodium cacodylate trihydrate pH 5.5, 35% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.002 M Hexammine cobalt(III) chloride
Crystal Properties Matthews coefficient Solvent content 1.96 37.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.006 α = 90 b = 41.006 β = 90 c = 123.438 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 PILATUS3 2M 2024-12-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97741 ALS 5.0.1
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 1.32 50 96.9 0.06 0.064 0.021 0.992 30.3 9.4 9461
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 1.32 1.34 88.7 0.511 0.543 0.18 0.902 4 8.6
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 1.32 34.128 9356 438 95.792 0.184 0.1828 0.1897 0.2065 0.2079 11.904
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 5.306 r_lrange_other 4.654 r_angle_refined_deg 2.297 r_scangle_it 1.815 r_scangle_other 1.813 r_scbond_it 1.297 r_scbond_other 1.295 r_angle_other_deg 0.694 r_nbtor_refined 0.255 r_xyhbond_nbd_refined 0.253
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.306 r_lrange_other 4.654 r_angle_refined_deg 2.297 r_scangle_it 1.815 r_scangle_other 1.813 r_scbond_it 1.297 r_scbond_other 1.295 r_angle_other_deg 0.694 r_nbtor_refined 0.255 r_xyhbond_nbd_refined 0.253 r_symmetry_nbd_other 0.203 r_symmetry_xyhbond_nbd_refined 0.155 r_nbd_other 0.143 r_nbd_refined 0.092 r_chiral_restr 0.091 r_symmetry_nbd_refined 0.087 r_symmetry_nbtor_other 0.084 r_metal_ion_refined 0.08 r_dihedral_angle_other_2_deg 0.069 r_gen_planes_refined 0.029 r_bond_refined_d 0.01 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 109 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing