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16mer self-complementary duplex RNA with dG:C 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 5.8 293 0.4 M Sodium chloride, 0.12 M Calcium chloride, 20 mM MES pH 5.8, 27% v/v (+/-)-2-Methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.03 39.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.511 α = 90 b = 41.511 β = 90 c = 124.629 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 2024-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.97648 ALS 5.0.3
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 1.375 50 99.5 0.067 0.072 0.027 0.972 26 7.2 8922
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 1.375 1.4 96.2 0.494 0.548 0.232 0.861 2.8 5.2
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.375 41.543 8380 389 93.652 0.179 0.1768 0.2154 0.2518 10.616
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] 0.004 0.002 0.004 -0.015
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 4.709 r_lrange_other 4.208 r_angle_refined_deg 1.859 r_scangle_it 1.636 r_scangle_other 1.634 r_scbond_it 1.14 r_scbond_other 1.139 r_angle_other_deg 0.541 r_nbtor_refined 0.25 r_xyhbond_nbd_refined 0.209
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 4.709 r_lrange_other 4.208 r_angle_refined_deg 1.859 r_scangle_it 1.636 r_scangle_other 1.634 r_scbond_it 1.14 r_scbond_other 1.139 r_angle_other_deg 0.541 r_nbtor_refined 0.25 r_xyhbond_nbd_refined 0.209 r_symmetry_nbd_other 0.196 r_symmetry_xyhbond_nbd_refined 0.191 r_metal_ion_refined 0.153 r_nbd_other 0.122 r_dihedral_angle_other_2_deg 0.112 r_symmetry_nbd_refined 0.093 r_nbd_refined 0.084 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.074 r_gen_planes_refined 0.028 r_bond_refined_d 0.009 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 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing