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Crystal structure of SARS-CoV-2 Mpro in complex with RK-240
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, pH6.0, 25% w/v, PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.79 55.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.093 α = 90 b = 80.382 β = 114.341 c = 51.635 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 2023-11-23 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 1.5 43.242 97.05 1 28.7 3.9 56677
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 1.5 1.554 0.976 4.29
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 1.5 43.242 56673 2851 97.058 0.18 0.1789 0.1886 0.2042 0.2143 20.194
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] 0.84 -0.821 2.127 -1.577
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.729 r_dihedral_angle_3_deg 15.237 r_dihedral_angle_2_deg 12.315 r_dihedral_angle_1_deg 6.552 r_lrange_it 6.213 r_lrange_other 6.166 r_scangle_it 4.923 r_scangle_other 4.922 r_dihedral_angle_other_3_deg 3.816 r_scbond_it 3.257
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.729 r_dihedral_angle_3_deg 15.237 r_dihedral_angle_2_deg 12.315 r_dihedral_angle_1_deg 6.552 r_lrange_it 6.213 r_lrange_other 6.166 r_scangle_it 4.923 r_scangle_other 4.922 r_dihedral_angle_other_3_deg 3.816 r_scbond_it 3.257 r_scbond_other 3.256 r_mcangle_it 3.093 r_mcangle_other 3.092 r_mcbond_it 2.197 r_mcbond_other 2.197 r_angle_refined_deg 1.773 r_angle_other_deg 0.604 r_nbd_refined 0.216 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.186 r_nbd_other 0.161 r_symmetry_nbd_refined 0.149 r_xyhbond_nbd_refined 0.131 r_symmetry_xyhbond_nbd_refined 0.117 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.086 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2329 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing