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Crystal structure of SARS-CoV-2 Mpro in complex with RK-384
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 SPG, pH 8.0, 25% w/v PEG 1500
Crystal Properties Matthews coefficient Solvent content 1.95 36.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.367 α = 90 b = 53.438 β = 102.913 c = 44.486 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 2023-09-26 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 1.75 48.11 98.65 0.999 17.68 6.9 25986
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 1.75 1.813 0.841
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 1.75 48.11 25986 1311 98.358 0.181 0.1782 0.1889 0.2369 0.2458 25.587
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] 1.152 -1.698 -0.439 0.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.922 r_dihedral_angle_3_deg 14.746 r_dihedral_angle_2_deg 11.019 r_dihedral_angle_1_deg 7.218 r_lrange_other 6.633 r_lrange_it 6.626 r_scangle_it 5.212 r_scangle_other 5.211 r_scbond_it 3.429 r_scbond_other 3.428
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.922 r_dihedral_angle_3_deg 14.746 r_dihedral_angle_2_deg 11.019 r_dihedral_angle_1_deg 7.218 r_lrange_other 6.633 r_lrange_it 6.626 r_scangle_it 5.212 r_scangle_other 5.211 r_scbond_it 3.429 r_scbond_other 3.428 r_mcangle_it 3.403 r_mcangle_other 3.403 r_mcbond_it 2.369 r_mcbond_other 2.364 r_dihedral_angle_other_3_deg 2.31 r_angle_refined_deg 1.528 r_angle_other_deg 0.542 r_nbd_refined 0.215 r_symmetry_nbd_other 0.199 r_nbd_other 0.195 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.149 r_symmetry_xyhbond_nbd_refined 0.131 r_symmetry_nbd_refined 0.111 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.078 r_gen_planes_refined 0.008 r_bond_refined_d 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 2358 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing