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Crystal structure of SARS-CoV-2 Mpro in complex with RK-54
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 293 0.1 M MMT pH 9.0, 25% w/v PEG 1500
Crystal Properties Matthews coefficient Solvent content 1.97 37.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.702 α = 90 b = 53.197 β = 102.445 c = 44.856 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 EIGER X 16M 2023-06-08 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 2.45 47.97 98.34 0.993 6.2 7 9623
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 2.45 2.538 0.559
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 2.45 47.97 9623 472 98.385 0.22 0.2156 0.2267 0.3052 0.3129 52.056
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] 7.946 0.449 -2.431 -5.206
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.007 r_dihedral_angle_6_deg 15.024 r_dihedral_angle_2_deg 9.097 r_lrange_it 9.013 r_lrange_other 9.012 r_dihedral_angle_1_deg 7.819 r_scangle_it 5.933 r_scangle_other 5.932 r_mcangle_other 5.199 r_mcangle_it 5.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.007 r_dihedral_angle_6_deg 15.024 r_dihedral_angle_2_deg 9.097 r_lrange_it 9.013 r_lrange_other 9.012 r_dihedral_angle_1_deg 7.819 r_scangle_it 5.933 r_scangle_other 5.932 r_mcangle_other 5.199 r_mcangle_it 5.198 r_scbond_it 3.489 r_scbond_other 3.488 r_mcbond_it 3.268 r_mcbond_other 3.264 r_dihedral_angle_other_2_deg 2.878 r_angle_refined_deg 1.102 r_dihedral_angle_other_3_deg 1.063 r_angle_other_deg 0.385 r_nbd_refined 0.229 r_symmetry_nbd_other 0.211 r_nbd_other 0.194 r_nbtor_refined 0.188 r_symmetry_nbd_refined 0.183 r_xyhbond_nbd_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.17 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.048 r_symmetry_xyhbond_nbd_other 0.037 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2358 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing