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Crystal structure of SARS CoV2 main protease in complex with DN_EG_002 (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 DN_EG_002 100 mM in 100% DMSO
Crystals were soaked for 3 hours with final concentration of 10 mM DN_EG_002 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 2.61 52.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.941 α = 90 b = 99.743 β = 90 c = 104.126 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 2020-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00003 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 2.065 49.423 99.82 0.158 0.164 0.044 0.998 11 13.5 44110
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 2.065 2.119 98.9 1.961 0.54 0.71 1.6 13.75
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 2.065 49.423 44049 2203 99.814 0.196 0.1949 0.1947 0.2275 0.2285 RANDOM 42.474
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] -1.753 2.332 -0.579
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.887 r_dihedral_angle_4_deg 15.226 r_dihedral_angle_3_deg 15.116 r_lrange_it 8.672 r_lrange_other 8.668 r_dihedral_angle_1_deg 7.582 r_scangle_it 6.911 r_scangle_other 6.91 r_mcangle_it 5.07 r_mcangle_other 5.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.887 r_dihedral_angle_4_deg 15.226 r_dihedral_angle_3_deg 15.116 r_lrange_it 8.672 r_lrange_other 8.668 r_dihedral_angle_1_deg 7.582 r_scangle_it 6.911 r_scangle_other 6.91 r_mcangle_it 5.07 r_mcangle_other 5.07 r_scbond_it 4.57 r_scbond_other 4.569 r_mcbond_other 3.543 r_mcbond_it 3.54 r_angle_refined_deg 1.633 r_angle_other_deg 1.369 r_nbd_other 0.256 r_symmetry_nbd_refined 0.224 r_nbd_refined 0.2 r_symmetry_nbd_other 0.192 r_symmetry_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.153 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4687 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDS data processing Coot model building PHASER phasing pointless data scaling XDS data reduction