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SARS-CoV2 Main Protease (Mpro) in complex with the covalent inhibitor 28a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y2E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290.15 22-27% PEG1500, 100mM MTT buffer [DL-Malic acid, 4-Morpholine
Ethane Sulfonic acid (MES) monohydrate, 2-Amino-2-
(hydroxymethyl)-1,3- propanediol (TRIS)-HCl), pH=6.0].
Crystal Properties Matthews coefficient Solvent content 1.96 37.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.914 α = 90 b = 53.134 β = 101.158 c = 114.429 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 100 PIXEL DECTRIS EIGER2 X 9M 2022-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8731 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 48.073 99.32 0.084 0.995 7.6 3.6 20880
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.968 0.9 0.299
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 1.9 48.073 20879 1078 99.348 0.258 0.2563 0.2593 0.2931 0.2922 34.213
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] -0.113 0.721 0.231 -0.373
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.51 r_dihedral_angle_other_2_deg 14.435 r_dihedral_angle_3_deg 12.587 r_dihedral_angle_6_deg 12.389 r_dihedral_angle_1_deg 6.565 r_lrange_it 4.022 r_lrange_other 3.991 r_scangle_it 1.974 r_scangle_other 1.974 r_mcangle_other 1.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.51 r_dihedral_angle_other_2_deg 14.435 r_dihedral_angle_3_deg 12.587 r_dihedral_angle_6_deg 12.389 r_dihedral_angle_1_deg 6.565 r_lrange_it 4.022 r_lrange_other 3.991 r_scangle_it 1.974 r_scangle_other 1.974 r_mcangle_other 1.814 r_mcangle_it 1.813 r_angle_refined_deg 1.232 r_scbond_it 1.203 r_scbond_other 1.202 r_angle_other_deg 1.164 r_mcbond_it 1.129 r_mcbond_other 1.125 r_symmetry_nbd_other 0.217 r_nbd_other 0.215 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.202 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.111 r_symmetry_nbd_refined 0.102 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.064 r_symmetry_xyhbond_nbd_other 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.009 r_bond_refined_d 0.007 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2398 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing