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Crystal structure of SARS-CoV-2 Mpro in complex with RK-491
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 7.5 293 0.1M Sodium HEPES; MOPS (acid) pH7.5, 30% v/v 40% v/v PEG 500 MME; 20 % w/v PEG 200001, 0.12M Ethylene glycols
Crystal Properties Matthews coefficient Solvent content 2.62 53.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.567 α = 90 b = 100.472 β = 90 c = 103.406 γ = 90
Symmetry Space Group P 21 21 21
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 2025-10-09 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 1.68 45.97 95.95 0.999 14.42 13.4 80677
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 1.68 1.74 0.636
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 1.68 45.97 80677 3870 96.847 0.244 0.2427 0.2558 0.2647 0.2753 28.015
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] -2.118 3.012 -0.894
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.708 r_dihedral_angle_3_deg 15.686 r_dihedral_angle_2_deg 7.671 r_dihedral_angle_1_deg 7.304 r_lrange_it 6.286 r_lrange_other 6.282 r_dihedral_angle_other_2_deg 5.398 r_scangle_it 4.607 r_scangle_other 4.606 r_mcangle_other 3.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.708 r_dihedral_angle_3_deg 15.686 r_dihedral_angle_2_deg 7.671 r_dihedral_angle_1_deg 7.304 r_lrange_it 6.286 r_lrange_other 6.282 r_dihedral_angle_other_2_deg 5.398 r_scangle_it 4.607 r_scangle_other 4.606 r_mcangle_other 3.63 r_mcangle_it 3.629 r_scbond_it 2.958 r_scbond_other 2.958 r_mcbond_it 2.452 r_mcbond_other 2.448 r_angle_refined_deg 1.482 r_dihedral_angle_other_3_deg 0.89 r_angle_other_deg 0.502 r_nbd_refined 0.211 r_symmetry_nbd_other 0.196 r_nbd_other 0.196 r_nbtor_refined 0.184 r_symmetry_nbd_refined 0.137 r_xyhbond_nbd_refined 0.133 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_refined 0.083 r_chiral_restr 0.069 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 4691 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing