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SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor E9
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% PEG 4000, 0.1 M MES, 5% DMSO
Crystal Properties Matthews coefficient Solvent content 2.57 52.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.82 α = 90 b = 99.305 β = 90 c = 103.252 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 2023-10-04 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) 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 1.65 56.75 99.98 0.177 0.184 0.05 0.997 8.4 13.5 84761
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 1.65 1.68 0.34
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 2.1 56.749 41418 968 99.947 0.192 0.1909 0.1921 0.2264 0.2277 36.606
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] -2.759 3.602 -0.843
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.58 r_dihedral_angle_3_deg 12.683 r_dihedral_angle_1_deg 6.916 r_lrange_it 6.261 r_dihedral_angle_2_deg 6.009 r_scangle_it 4.55 r_scbond_it 3.114 r_mcangle_it 2.839 r_angle_refined_deg 1.897 r_mcbond_it 1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.58 r_dihedral_angle_3_deg 12.683 r_dihedral_angle_1_deg 6.916 r_lrange_it 6.261 r_dihedral_angle_2_deg 6.009 r_scangle_it 4.55 r_scbond_it 3.114 r_mcangle_it 2.839 r_angle_refined_deg 1.897 r_mcbond_it 1.88 r_nbtor_refined 0.318 r_nbd_refined 0.217 r_symmetry_xyhbond_nbd_refined 0.195 r_symmetry_nbd_refined 0.184 r_xyhbond_nbd_refined 0.131 r_ncsr_local_group_1 0.117 r_chiral_restr 0.108 r_ext_dist_refined_b 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4581 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement DIALS data reduction pointless data scaling PHASER phasing