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Structure of the SARS-CoV-2 3CL protease in complex with rupintrivir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other SARS-CoV-2 3CL protease
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 Triammonium citrate, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.03 39.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.023 α = 90 b = 54.024 β = 100.774 c = 114.067 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS PILATUS 6M 2020-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.256 56.091 84.4 0.998 9.6 2.5 21599
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.256 2.295 0.58
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 FREE R-VALUE SARS-CoV-2 3CL protease 2.256 56.091 21599 1115 84.388 0.203 0.2 0.2058 0.2581 0.2657 50.928
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] 0.047 0.022 -0.034 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.343 r_dihedral_angle_4_deg 19.495 r_dihedral_angle_other_3_deg 17.903 r_dihedral_angle_3_deg 16.103 r_lrange_it 9.868 r_lrange_other 9.867 r_dihedral_angle_1_deg 8.117 r_scangle_it 6.215 r_scangle_other 6.214 r_mcangle_it 5.511
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.343 r_dihedral_angle_4_deg 19.495 r_dihedral_angle_other_3_deg 17.903 r_dihedral_angle_3_deg 16.103 r_lrange_it 9.868 r_lrange_other 9.867 r_dihedral_angle_1_deg 8.117 r_scangle_it 6.215 r_scangle_other 6.214 r_mcangle_it 5.511 r_mcangle_other 5.511 r_scbond_it 4.06 r_scbond_other 4.059 r_mcbond_it 3.643 r_mcbond_other 3.638 r_angle_refined_deg 1.471 r_angle_other_deg 1.222 r_nbd_other 0.212 r_nbd_refined 0.204 r_symmetry_nbd_other 0.195 r_symmetry_nbd_refined 0.184 r_symmetry_xyhbond_nbd_refined 0.18 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.129 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4694 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing