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16mer self-complementary duplex RNA with dA:s(2)U pair sequence 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9MDY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 0.02 M Calcium chloride dihydrate, 0.1 M Sodium acetate trihydrate pH 4.6, 30% v/v (+/-)-2-Methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 1.99 38.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.147 α = 90 b = 41.147 β = 90 c = 124.373 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 2024-10-30 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 1.23 50 96.2 0.04 0.043 0.014 1 52 8.3 11714
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 1.23 1.25 62.3 0.214 0.251 0.127 0.945 5.2 3.4
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 1.233 41.458 11595 586 95.771 0.185 0.1834 0.1902 0.2273 0.2351 12.1
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] -0.003 -0.002 -0.003 0.01
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.831 r_lrange_other 4.898 r_angle_refined_deg 2.044 r_scangle_it 1.567 r_scangle_other 1.566 r_scbond_it 1.134 r_scbond_other 1.133 r_angle_other_deg 0.828 r_nbd_refined 0.42 r_xyhbond_nbd_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.831 r_lrange_other 4.898 r_angle_refined_deg 2.044 r_scangle_it 1.567 r_scangle_other 1.566 r_scbond_it 1.134 r_scbond_other 1.133 r_angle_other_deg 0.828 r_nbd_refined 0.42 r_xyhbond_nbd_refined 0.295 r_symmetry_nbd_other 0.276 r_nbtor_refined 0.242 r_symmetry_xyhbond_nbd_refined 0.228 r_chiral_restr_other 0.22 r_nbd_other 0.13 r_chiral_restr 0.084 r_symmetry_nbd_refined 0.082 r_symmetry_nbtor_other 0.073 r_dihedral_angle_other_2_deg 0.059 r_gen_planes_refined 0.03 r_bond_other_d 0.025 r_bond_refined_d 0.013 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 335 Solvent Atoms 107 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing