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Human Argonaute3 bound to cityRNA and target RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VM9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.8 293.15 0.14 M sodium citrate, 0.1 M Bis-Tris propane pH 8.8, and 18% (w/v) PEG 3350 supplemented with 4% (v/v) 1,3-Propanediol
Crystal Properties Matthews coefficient Solvent content 3.05 59.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.142 α = 90 b = 138.126 β = 90 c = 143.533 γ = 90
Symmetry Space Group P 2 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 16M 2022-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97934 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 3.45 48.23 99.5 0.239 7.1 6.6 17731 107.03
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.45 3.573 1.527
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.45 48.23 1.34 17661 1804 99.53 0.2109 0.206 0.2095 0.2543 0.2226 137.61
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.6953 f_angle_d 0.6884 f_chiral_restr 0.0439 f_plane_restr 0.0058 f_bond_d 0.0036
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6617 Nucleic Acid Atoms 485 Solvent Atoms 25 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Coot model building PHASER phasing XDS data scaling XDS data reduction