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Crystal structure of SARS-CoV-2 3CL protease in complex with compound 1
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 0.02 M Sodium/potassium phosphate 0.1 M Bis-Tris propane 7.5 20 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.48 50.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.83 α = 90 b = 101.249 β = 90 c = 104.18 γ = 90
Symmetry Space Group P 21 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 173 PIXEL RIGAKU HyPix-6000HE 2024-08-22 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 2.2 30.23 99.9 0.184 0.193 0.058 0.993 9.1 10.9 37147
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 2.2 2.27 100 0.545 0.575 0.18 0.925 10
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.2 30.23 35092 1752 99.22 0.22476 0.22255 0.26844 0.2517 RANDOM 24.741
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] -2.27 2.13 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.821 r_dihedral_angle_1_deg 7.444 r_long_range_B_refined 5.839 r_long_range_B_other 5.838 r_dihedral_angle_2_deg 5.711 r_scangle_other 4.036 r_mcangle_it 3.512 r_mcangle_other 3.511 r_scbond_it 2.501 r_scbond_other 2.501
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.821 r_dihedral_angle_1_deg 7.444 r_long_range_B_refined 5.839 r_long_range_B_other 5.838 r_dihedral_angle_2_deg 5.711 r_scangle_other 4.036 r_mcangle_it 3.512 r_mcangle_other 3.511 r_scbond_it 2.501 r_scbond_other 2.501 r_mcbond_it 2.218 r_mcbond_other 2.218 r_angle_refined_deg 1.668 r_angle_other_deg 0.589 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.002 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 4474 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing CrysalisPro data reduction