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SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor E2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YB7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 11% PEG4000, 0.1 M MES, 5% DMSO
Crystal Properties Matthews coefficient Solvent content 2.54 51.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.75 α = 90 b = 98.03 β = 90 c = 102.67 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 100 PIXEL DECTRIS EIGER2 X 16M 2023-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
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 2.29 39.75 100 0.989 4.89 13.5 31517
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 2.29 2.33 100 0.0332 0.03457 0.96 0.356 12.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.5 39.743 24278 1286 99.951 0.198 0.1947 0.1967 0.2455 0.2471 46.474
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] -3.466 4.175 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.571 r_dihedral_angle_3_deg 15.744 r_dihedral_angle_6_deg 14.446 r_lrange_it 8.537 r_dihedral_angle_1_deg 7.571 r_scangle_it 6.499 r_scbond_it 4.574 r_mcangle_it 4.449 r_mcbond_it 2.989 r_angle_refined_deg 2.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.571 r_dihedral_angle_3_deg 15.744 r_dihedral_angle_6_deg 14.446 r_lrange_it 8.537 r_dihedral_angle_1_deg 7.571 r_scangle_it 6.499 r_scbond_it 4.574 r_mcangle_it 4.449 r_mcbond_it 2.989 r_angle_refined_deg 2.049 r_nbtor_refined 0.318 r_nbd_refined 0.227 r_symmetry_nbd_refined 0.213 r_xyhbond_nbd_refined 0.154 r_ncsr_local_group_1 0.13 r_symmetry_xyhbond_nbd_refined 0.121 r_chiral_restr 0.118 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4622 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement xia2 data reduction pointless data scaling PHASER phasing