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Crystal structure of the SARS-CoV-2 Omicron main protease (Mpro) in complex with inhibitor GC376
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7LYH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% PEG 3350, 0.2 M KNO3
Crystal Properties Matthews coefficient Solvent content 1.96 37.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.186 α = 90 b = 52.987 β = 100.5 c = 113.006 γ = 90
Symmetry Space Group I 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 R 4M 2022-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54056
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.05 26.21 99.2 0.077 0.092 0.05 0.992 9.4 3.3 16446
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.11 98.4 0.499 0.613 0.352 0.692 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7lyh 2.05 26.21 15614 829 98.89 0.1737 0.1716 0.1795 0.2135 0.2173 RANDOM 30.736
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] -1.28 -0.3 -0.31 1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.171 r_dihedral_angle_4_deg 22.893 r_dihedral_angle_3_deg 13.594 r_dihedral_angle_1_deg 7.603 r_angle_other_deg 1.678 r_angle_refined_deg 1.543 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.171 r_dihedral_angle_4_deg 22.893 r_dihedral_angle_3_deg 13.594 r_dihedral_angle_1_deg 7.603 r_angle_other_deg 1.678 r_angle_refined_deg 1.543 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2363 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction MOLREP phasing