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Crystal structure of SARS-CoV-2 Mpro-H172Y 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 0.1M Bis Tris Propane pH 6.5, 0.2 MSodium acetate trihydrate, 20 % w/vPEG 3350, 10% v/vEthylene glycol
Crystal Properties Matthews coefficient Solvent content 2.04 39.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.398 α = 90 b = 54.273 β = 100.777 c = 45.021 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 6M-F 2022-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.003 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 44.23 98.7 0.999 12 4.9 18059 39.23
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 2.072 0.527 1.34
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 2 44.23 18059 933 98.489 0.211 0.2077 0.214 0.2712 0.2791 43.513
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] 0.833 1.041 -0.565 -0.619
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.439 r_dihedral_angle_4_deg 17.417 r_dihedral_angle_3_deg 17.003 r_lrange_other 8.795 r_lrange_it 8.783 r_dihedral_angle_1_deg 8.43 r_scangle_it 6.734 r_scangle_other 6.734 r_mcangle_it 5.403 r_mcangle_other 5.378
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.439 r_dihedral_angle_4_deg 17.417 r_dihedral_angle_3_deg 17.003 r_lrange_other 8.795 r_lrange_it 8.783 r_dihedral_angle_1_deg 8.43 r_scangle_it 6.734 r_scangle_other 6.734 r_mcangle_it 5.403 r_mcangle_other 5.378 r_scbond_it 4.689 r_scbond_other 4.687 r_mcbond_it 3.937 r_mcbond_other 3.913 r_angle_refined_deg 1.621 r_angle_other_deg 1.317 r_symmetry_xyhbond_nbd_refined 0.224 r_nbd_refined 0.21 r_nbd_other 0.192 r_symmetry_nbd_refined 0.191 r_symmetry_nbd_other 0.189 r_xyhbond_nbd_refined 0.177 r_nbtor_refined 0.17 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.072 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 2335 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing