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Crystal structure of SARS CoV2 main protease in complex with EG009 (modelled using PanDDA event map)
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 6.5 293 0.1 M MES pH 6.5
15% w/v PEG 6000
5% v/v MPD
Compound stock EG009 100 mM in 100% DMSO
Crystals were soaked for 3 hours with final concentration of 10 mM EG009 by adding the stock to crystallisation drops in a 1/10 ratio yielding 10% (V/V) final DMSO concentration.
Crystal Properties Matthews coefficient Solvent content 2.6439114 53.506916
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.979 α = 90 b = 100.929 β = 90 c = 104.183 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 EIGER X 16M 2020-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00036 SLS X06SA
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 2.19 46.29 99.3 0.254 0.264 0.071 0.997 9.6 13.5 37312
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.19 2.26 98.7 2.587 0.741 0.699 1.4 13.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6lu7 2.19 46.29 37256 1862 99.088 0.218 0.2155 0.2181 0.2608 0.2598 RANDOM 38.769
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] -3.603 5.503 -1.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.9 r_dihedral_angle_3_deg 16.7 r_dihedral_angle_4_deg 16.283 r_dihedral_angle_1_deg 7.796 r_lrange_it 7.128 r_lrange_other 7.125 r_scangle_it 5.284 r_scangle_other 5.284 r_mcangle_it 4.26 r_mcangle_other 4.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.9 r_dihedral_angle_3_deg 16.7 r_dihedral_angle_4_deg 16.283 r_dihedral_angle_1_deg 7.796 r_lrange_it 7.128 r_lrange_other 7.125 r_scangle_it 5.284 r_scangle_other 5.284 r_mcangle_it 4.26 r_mcangle_other 4.26 r_scbond_it 3.112 r_scbond_other 3.111 r_mcbond_it 2.558 r_mcbond_other 2.554 r_angle_refined_deg 1.54 r_angle_other_deg 1.272 r_nbd_other 0.214 r_symmetry_nbd_refined 0.203 r_nbd_refined 0.193 r_symmetry_xyhbond_nbd_refined 0.193 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.16 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.069 r_symmetry_xyhbond_nbd_other 0.046 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4725 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building