☰ Navigation Tabs
16mer self-complementary duplex RNA with s(2)U:A 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 7.5 298 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 1.95 36.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.995 α = 90 b = 40.995 β = 90 c = 122.92 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 1.36 50 100 0.044 0.047 0.016 0.999 49.4 9.2 8888
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 1.36 1.38 100 0.493 0.533 0.201 0.899 3.4 6.7
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 1.36 40.973 8856 413 99.394 0.187 0.1856 0.1902 0.2175 0.2234 12.214
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 0.013
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 6.866 r_lrange_other 6.333 r_angle_other_deg 3.073 r_angle_refined_deg 2.25 r_chiral_restr_other 2.144 r_scangle_it 1.978 r_scangle_other 1.976 r_scbond_it 1.423 r_scbond_other 1.421 r_nbtor_refined 0.25
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 6.866 r_lrange_other 6.333 r_angle_other_deg 3.073 r_angle_refined_deg 2.25 r_chiral_restr_other 2.144 r_scangle_it 1.978 r_scangle_other 1.976 r_scbond_it 1.423 r_scbond_other 1.421 r_nbtor_refined 0.25 r_xyhbond_nbd_refined 0.223 r_symmetry_nbd_other 0.199 r_symmetry_xyhbond_nbd_refined 0.196 r_nbd_other 0.167 r_symmetry_nbd_refined 0.101 r_chiral_restr 0.091 r_nbd_refined 0.087 r_metal_ion_refined 0.079 r_symmetry_nbtor_other 0.075 r_dihedral_angle_other_2_deg 0.062 r_bond_other_d 0.033 r_gen_planes_refined 0.029 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 336 Solvent Atoms 100 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing