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Crystal structure of the Mpro of SARS COV-2 in complex with the MG-87 inhibitor
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 8.5 293 0.02 M sodium/potassium phosphate, 0.1 M Bis Tris propane pH8.5, 20 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.24 45.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.941 α = 90 b = 63.773 β = 91.251 c = 103.513 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 2021-11-24 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 2.19 45.972 98.6 0.996 10.9 6.9 30543
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 2.19 2.26 0.852
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.19 45.972 30543 1411 98.58 0.169 0.1664 0.2184 0.215 26.817
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] -0.98 0.086 0.061 0.915
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.058 r_dihedral_angle_6_deg 15.708 r_dihedral_angle_2_deg 9.487 r_dihedral_angle_1_deg 7.611 r_lrange_other 6.726 r_lrange_it 6.725 r_scangle_it 5.106 r_scangle_other 5.106 r_dihedral_angle_other_3_deg 4.427 r_mcangle_other 3.481
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.058 r_dihedral_angle_6_deg 15.708 r_dihedral_angle_2_deg 9.487 r_dihedral_angle_1_deg 7.611 r_lrange_other 6.726 r_lrange_it 6.725 r_scangle_it 5.106 r_scangle_other 5.106 r_dihedral_angle_other_3_deg 4.427 r_mcangle_other 3.481 r_mcangle_it 3.477 r_scbond_it 3.166 r_scbond_other 3.165 r_mcbond_it 2.253 r_mcbond_other 2.252 r_angle_refined_deg 1.419 r_angle_other_deg 0.472 r_symmetry_nbd_refined 0.217 r_nbd_refined 0.204 r_symmetry_nbd_other 0.196 r_nbd_other 0.19 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.151 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.066 r_symmetry_xyhbond_nbd_refined 0.058 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4734 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing