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Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor Jun10221
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 25% PEG 3350, 0.2 M AmSO4, 0.1 M HEPES 7.5
Crystal Properties Matthews coefficient Solvent content 2 38.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.16 α = 90 b = 53.355 β = 100.67 c = 114.462 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 100 PIXEL DECTRIS PILATUS3 6M 2022-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.55 50 92.8 0.962 6.7 2.2 32064
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.59 94 0.64 2
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 2.54 48.25 16373 827 96.04 0.22029 0.21816 0.2205 0.26267 0.2674 RANDOM 52.893
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] 0.03 0.06 -0.45 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.631 r_dihedral_angle_4_deg 17.864 r_dihedral_angle_3_deg 15.942 r_long_range_B_refined 8.687 r_long_range_B_other 8.686 r_dihedral_angle_1_deg 7.382 r_mcangle_it 6.238 r_mcangle_other 6.237 r_scangle_other 6.066 r_mcbond_it 4.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.631 r_dihedral_angle_4_deg 17.864 r_dihedral_angle_3_deg 15.942 r_long_range_B_refined 8.687 r_long_range_B_other 8.686 r_dihedral_angle_1_deg 7.382 r_mcangle_it 6.238 r_mcangle_other 6.237 r_scangle_other 6.066 r_mcbond_it 4.107 r_mcbond_other 4.101 r_scbond_it 4.006 r_scbond_other 4.006 r_angle_refined_deg 1.43 r_angle_other_deg 1.153 r_chiral_restr 0.054 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 4644 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 70
Software Software Software Name Purpose HKL-3000 data scaling REFMAC refinement HKL-3000 data reduction MOLREP phasing