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Mpro of SARS COV-2 in complex with the MG-97 inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y2E 6y2e
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M Bis Tris Propane pH 6.50, 2M Sodium formate, 20% w/vPEG 3350, 10% v/vEthylene glycol
Crystal Properties Matthews coefficient Solvent content 2.25 45.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.779 α = 90 b = 63.659 β = 91.057 c = 103.646 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 16M 2021-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
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 1.997 42.193 95.7 0.997 14.9 3.6 38735
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 2 2.07 95.5 0.976
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6y2e 1.997 42.193 38735 1909 95.366 0.163 0.1605 0.1714 0.206 0.2122 20.607
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] -0.012 0.004 -0.011 0.023
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.52 r_dihedral_angle_4_deg 15.856 r_dihedral_angle_3_deg 14.282 r_dihedral_angle_1_deg 7.463 r_lrange_it 5.989 r_lrange_other 5.912 r_scangle_it 4.24 r_scangle_other 4.24 r_scbond_it 2.733 r_scbond_other 2.733
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.52 r_dihedral_angle_4_deg 15.856 r_dihedral_angle_3_deg 14.282 r_dihedral_angle_1_deg 7.463 r_lrange_it 5.989 r_lrange_other 5.912 r_scangle_it 4.24 r_scangle_other 4.24 r_scbond_it 2.733 r_scbond_other 2.733 r_dihedral_angle_other_3_deg 2.679 r_mcangle_it 2.651 r_mcangle_other 2.65 r_mcbond_it 1.757 r_mcbond_other 1.757 r_angle_refined_deg 1.642 r_angle_other_deg 1.401 r_nbd_other 0.221 r_nbd_refined 0.203 r_symmetry_xyhbond_nbd_refined 0.195 r_symmetry_nbd_refined 0.19 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.135 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4705 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing