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16mer self-complementary duplex RNA with all Watson-Crick base pairs
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 7.5 298 20 % v/v Polyethylene glycol 200, 50 mM HEPES pH 7.5, 200 mM Potassium Chloride, 25 mM Magnesium Sulfate
Crystal Properties Matthews coefficient Solvent content 1.99 38.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.159 α = 90 b = 41.159 β = 90 c = 124.195 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 1.42 50 100 0.071 0.076 0.027 0.974 4.2 9 7975
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 1.42 1.44 100 0.481 0.511 0.172 0.919 4.2 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 1.421 41.398 7944 386 99.611 0.183 0.1812 0.1865 0.2203 0.2211 11.113
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 -0.011
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.974 r_lrange_other 5.753 r_angle_refined_deg 1.977 r_scangle_it 1.802 r_scangle_other 1.801 r_scbond_it 1.261 r_scbond_other 1.259 r_angle_other_deg 0.716 r_nbtor_refined 0.243 r_xyhbond_nbd_refined 0.239
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.974 r_lrange_other 5.753 r_angle_refined_deg 1.977 r_scangle_it 1.802 r_scangle_other 1.801 r_scbond_it 1.261 r_scbond_other 1.259 r_angle_other_deg 0.716 r_nbtor_refined 0.243 r_xyhbond_nbd_refined 0.239 r_symmetry_nbd_other 0.193 r_symmetry_xyhbond_nbd_refined 0.167 r_nbd_other 0.14 r_nbd_refined 0.087 r_symmetry_nbd_refined 0.087 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.078 r_dihedral_angle_other_2_deg 0.05 r_gen_planes_refined 0.028 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 336 Solvent Atoms 98 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing