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Crystal structure of SARS-CoV-2 Mpro in complex with GK-730
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 7.5 294 0.02M Sodium potassium phosphate pH7.5, 20% w/v PEG 3350, 10% v/v Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.04 39.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.777 α = 90 b = 52.896 β = 98.94 c = 45.648 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 2024-05-03 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 1.9 48.01 98.96 0.998 9.19 13.8 21422
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 1.9 1.968 0.556
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.9 48.01 21420 1066 98.979 0.175 0.1723 0.2309 0.2142 30.805
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] 1.594 -1.996 -1.038 0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.939 r_dihedral_angle_3_deg 15.39 r_dihedral_angle_2_deg 15.065 r_lrange_it 7.839 r_lrange_other 7.824 r_dihedral_angle_1_deg 7.312 r_scangle_it 6.262 r_scangle_other 6.261 r_scbond_it 4.083 r_scbond_other 4.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.939 r_dihedral_angle_3_deg 15.39 r_dihedral_angle_2_deg 15.065 r_lrange_it 7.839 r_lrange_other 7.824 r_dihedral_angle_1_deg 7.312 r_scangle_it 6.262 r_scangle_other 6.261 r_scbond_it 4.083 r_scbond_other 4.082 r_mcangle_it 3.626 r_mcangle_other 3.626 r_dihedral_angle_other_3_deg 2.912 r_mcbond_it 2.755 r_mcbond_other 2.732 r_dihedral_angle_other_2_deg 2.42 r_angle_refined_deg 1.592 r_angle_other_deg 0.542 r_nbd_refined 0.217 r_symmetry_nbd_other 0.201 r_nbd_other 0.199 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.156 r_symmetry_nbd_refined 0.145 r_symmetry_xyhbond_nbd_refined 0.116 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.077 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 2367 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing