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Mpro of SARS COV-2 in complex with the MG-100 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 0.02 M sodium/potassium phosphate, 0.1 M Bis Tris propane pH6.5, 20 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.22 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.836 α = 90 b = 63.408 β = 91.103 c = 103.374 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 2.6 40.06 98.3 0.989 8 3.5 18139
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 2.6 2.69 0.721
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 2.6 40.06 18139 917 98.341 0.185 0.1815 0.1864 0.2517 0.2499 31.644
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] -0.201 -0.024 -0.056 0.258
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.581 r_dihedral_angle_3_deg 19.086 r_dihedral_angle_4_deg 16.905 r_dihedral_angle_1_deg 8.119 r_lrange_it 6.099 r_lrange_other 6.099 r_dihedral_angle_other_3_deg 4.546 r_scangle_it 3.851 r_scangle_other 3.85 r_mcangle_it 3.675
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.581 r_dihedral_angle_3_deg 19.086 r_dihedral_angle_4_deg 16.905 r_dihedral_angle_1_deg 8.119 r_lrange_it 6.099 r_lrange_other 6.099 r_dihedral_angle_other_3_deg 4.546 r_scangle_it 3.851 r_scangle_other 3.85 r_mcangle_it 3.675 r_mcangle_other 3.675 r_scbond_it 2.414 r_scbond_other 2.414 r_mcbond_it 2.255 r_mcbond_other 2.254 r_angle_refined_deg 1.594 r_angle_other_deg 1.234 r_symmetry_nbd_refined 0.234 r_nbd_refined 0.211 r_nbd_other 0.207 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.157 r_symmetry_xyhbond_nbd_other 0.141 r_symmetry_xyhbond_nbd_refined 0.104 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4734 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing