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Crystal structure of SARS-CoV-2 3CL protease in complex with compound 17 (S-892216)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LU7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Lithium sulfate monohydrate, 20% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 1.99 38.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.455 α = 90 b = 53.73 β = 98.88 c = 114.307 γ = 90
Symmetry Space Group I 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 173 PIXEL RIGAKU HyPix-6000HE 2022-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-X 1.54178
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 1.9 27.72 99.6 0.045 0.052 0.024 0.998 18.3 4.2 21030
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 1.9 1.95 97.8 0.206 0.261 0.157 0.755 2.6
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.9 27.72 19970 1060 99.54 0.19376 0.19119 0.1974 0.24172 0.2443 RANDOM 16.293
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] -0.3 0.27 -0.17 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.416 r_dihedral_angle_1_deg 7.336 r_long_range_B_refined 4.211 r_long_range_B_other 4.21 r_dihedral_angle_2_deg 3.085 r_scangle_other 2.903 r_mcangle_it 2.415 r_mcangle_other 2.415 r_scbond_it 1.988 r_scbond_other 1.988
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.416 r_dihedral_angle_1_deg 7.336 r_long_range_B_refined 4.211 r_long_range_B_other 4.21 r_dihedral_angle_2_deg 3.085 r_scangle_other 2.903 r_mcangle_it 2.415 r_mcangle_other 2.415 r_scbond_it 1.988 r_scbond_other 1.988 r_angle_refined_deg 1.773 r_mcbond_it 1.57 r_mcbond_other 1.57 r_angle_other_deg 0.723 r_chiral_restr 0.089 r_gen_planes_refined 0.011 r_bond_refined_d 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.004 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2249 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing CrysalisPro data reduction