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Crystal structure of SARS-CoV-2 Mpro in complex with GK729
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 0.2 M lithium chloride, 0.1 M Tris, 20% PEG 6000, 10% Ethylene glycol.
Crystal Properties Matthews coefficient Solvent content 2.65 53.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.749 α = 90 b = 102.788 β = 101.063 c = 104.697 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 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 1.55 46.04 98.79 0.999 10.84 7 201147
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 1.55 1.605 0.582
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 1.55 46.04 201144 10007 98.83 0.218 0.2163 0.2335 0.245 0.2628 26.718
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] -2.223 0.62 -1.373 3.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.471 r_dihedral_angle_3_deg 15.461 r_dihedral_angle_2_deg 8.476 r_dihedral_angle_1_deg 7.172 r_lrange_it 6.732 r_lrange_other 6.719 r_scangle_it 5.418 r_scangle_other 5.418 r_scbond_it 3.534 r_scbond_other 3.533
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.471 r_dihedral_angle_3_deg 15.461 r_dihedral_angle_2_deg 8.476 r_dihedral_angle_1_deg 7.172 r_lrange_it 6.732 r_lrange_other 6.719 r_scangle_it 5.418 r_scangle_other 5.418 r_scbond_it 3.534 r_scbond_other 3.533 r_mcangle_it 3.525 r_mcangle_other 3.525 r_dihedral_angle_other_2_deg 3.472 r_dihedral_angle_other_3_deg 2.873 r_mcbond_it 2.457 r_mcbond_other 2.457 r_angle_refined_deg 1.534 r_angle_other_deg 0.522 r_nbd_refined 0.211 r_nbd_other 0.196 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.184 r_symmetry_nbd_refined 0.179 r_xyhbond_nbd_other 0.169 r_symmetry_xyhbond_nbd_refined 0.155 r_xyhbond_nbd_refined 0.144 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.074 r_symmetry_xyhbond_nbd_other 0.023 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9430 Nucleic Acid Atoms Solvent Atoms 655 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing