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Crystal structure of SARS-CoV-2 Mpro-Q189K mutant, free enzyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other 6y2e
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.2M Sodium formate, 0.1M Bis-Tris propane pH6.5, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.05 39.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.75 α = 90 b = 106.633 β = 104.725 c = 53.589 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 2022-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.92 46.61 98.4 0.065 0.998 8.5 3.5 40519
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 1.92 1.97 0.587
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.92 46.61 40494 1966 98.277 0.239 0.2361 0.2514 0.2944 0.3113 47.455
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] 5.191 -1.458 -3.797 -0.552
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.707 r_dihedral_angle_3_deg 18.549 r_dihedral_angle_4_deg 18.003 r_lrange_it 9.198 r_lrange_other 9.198 r_dihedral_angle_1_deg 8.31 r_scangle_it 6.276 r_scangle_other 6.275 r_mcangle_it 6.001 r_mcangle_other 6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.707 r_dihedral_angle_3_deg 18.549 r_dihedral_angle_4_deg 18.003 r_lrange_it 9.198 r_lrange_other 9.198 r_dihedral_angle_1_deg 8.31 r_scangle_it 6.276 r_scangle_other 6.275 r_mcangle_it 6.001 r_mcangle_other 6 r_scbond_it 4.142 r_scbond_other 4.141 r_mcbond_it 4.138 r_mcbond_other 4.138 r_angle_refined_deg 1.594 r_angle_other_deg 1.254 r_nbd_other 0.24 r_nbd_refined 0.221 r_symmetry_nbd_refined 0.216 r_symmetry_nbd_other 0.197 r_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.129 r_symmetry_xyhbond_nbd_other 0.115 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.065 r_bond_refined_d 0.008 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 4696 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing