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Crystal Structure of the SARS-CoV-2 (COVID-19) main protease with inhibitor AD05
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7K3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289.15 0.1M Bis-Tris pH 6.5, 18% (v/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.62 53.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.52 α = 90 b = 80.14 β = 97.467 c = 88.966 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 PILATUS3 R 200K-A 2024-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 1.967 29.26 99.4 0.046 0.063 0.042 0.998 13.6 3.1 25354
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 1.97 2.02 0.144 0.196 0.131 0.958 2.8
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 1.967 23.683 25342 1278 99.264 0.178 0.1756 0.1734 0.2157 0.2078 23.932
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] -1.416 0.2 0.819 0.527
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.255 r_dihedral_angle_3_deg 13.653 r_dihedral_angle_2_deg 10.297 r_lrange_it 8.82 r_lrange_other 8.816 r_dihedral_angle_1_deg 7.462 r_scangle_it 6.939 r_scangle_other 6.937 r_scbond_it 4.878 r_mcangle_other 4.803
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.255 r_dihedral_angle_3_deg 13.653 r_dihedral_angle_2_deg 10.297 r_lrange_it 8.82 r_lrange_other 8.816 r_dihedral_angle_1_deg 7.462 r_scangle_it 6.939 r_scangle_other 6.937 r_scbond_it 4.878 r_mcangle_other 4.803 r_mcangle_it 4.801 r_scbond_other 4.755 r_mcbond_it 3.413 r_mcbond_other 3.413 r_dihedral_angle_other_2_deg 2.871 r_angle_refined_deg 2.541 r_angle_other_deg 0.839 r_nbd_refined 0.236 r_symmetry_nbd_other 0.213 r_xyhbond_nbd_refined 0.199 r_nbd_other 0.199 r_nbtor_refined 0.193 r_symmetry_xyhbond_nbd_refined 0.186 r_symmetry_nbd_refined 0.172 r_chiral_restr 0.124 r_symmetry_nbtor_other 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.014 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2329 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement Aimless data scaling iMOSFLM data reduction PHASER phasing