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Crystal structure of SARS-CoV-2 Mpro in complex with RK-452
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 6.5 293 0.1 M Bis-Tris, pH 6.5, 25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.14 42.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.252 α = 90 b = 123.422 β = 104.923 c = 71.582 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 2023-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03272 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 1.76 46.05 99.05 0.999 16.32 14 110393
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 1.76 1.823 0.75
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 1.76 46.05 110393 5651 99.011 0.176 0.1741 0.1881 0.2126 0.223 29.7
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] -0.532 -1.693 -1.318 2.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.324 r_dihedral_angle_3_deg 15.884 r_dihedral_angle_2_deg 7.952 r_dihedral_angle_1_deg 6.982 r_lrange_it 6.441 r_lrange_other 6.414 r_scangle_it 5.068 r_scangle_other 5.068 r_scbond_it 3.35 r_scbond_other 3.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.324 r_dihedral_angle_3_deg 15.884 r_dihedral_angle_2_deg 7.952 r_dihedral_angle_1_deg 6.982 r_lrange_it 6.441 r_lrange_other 6.414 r_scangle_it 5.068 r_scangle_other 5.068 r_scbond_it 3.35 r_scbond_other 3.35 r_dihedral_angle_other_2_deg 3.323 r_mcangle_it 3.26 r_mcangle_other 3.259 r_mcbond_it 2.34 r_mcbond_other 2.34 r_dihedral_angle_other_3_deg 2.244 r_angle_refined_deg 1.404 r_angle_other_deg 0.486 r_nbd_refined 0.208 r_symmetry_nbd_other 0.195 r_nbd_other 0.19 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.162 r_xyhbond_nbd_refined 0.142 r_symmetry_nbd_refined 0.139 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.07 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9400 Nucleic Acid Atoms Solvent Atoms 633 Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing