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Crystal Structure of the SARS-CoV-2 (COVID-19) main protease with inhibitor AD06
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 pH6.5, 18% (v/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.87 34.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.15 α = 90 b = 52.89 β = 101.799 c = 110.62 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 2024-11-26 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 27.16 98.7 0.13 0.176 0.118 0.987 4.3 3.1 18445
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 0.822 1.081 0.695 0.709 3
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 23.773 18428 942 98.503 0.232 0.228 0.2208 0.3157 0.3015 33.963
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] -0.918 -0.827 -2.774 3.714
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.092 r_dihedral_angle_3_deg 16.435 r_dihedral_angle_6_deg 14.602 r_lrange_it 10.557 r_lrange_other 10.555 r_scangle_it 9 r_scangle_other 8.998 r_dihedral_angle_1_deg 8.387 r_dihedral_angle_other_2_deg 7.322 r_scbond_it 6.599
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.092 r_dihedral_angle_3_deg 16.435 r_dihedral_angle_6_deg 14.602 r_lrange_it 10.557 r_lrange_other 10.555 r_scangle_it 9 r_scangle_other 8.998 r_dihedral_angle_1_deg 8.387 r_dihedral_angle_other_2_deg 7.322 r_scbond_it 6.599 r_mcangle_it 6.552 r_mcangle_other 6.55 r_scbond_other 6.487 r_mcbond_other 4.962 r_mcbond_it 4.961 r_angle_refined_deg 2.774 r_angle_other_deg 0.89 r_nbd_refined 0.254 r_symmetry_nbd_other 0.234 r_symmetry_xyhbond_nbd_refined 0.228 r_nbd_other 0.226 r_nbtor_refined 0.206 r_symmetry_nbd_refined 0.198 r_xyhbond_nbd_refined 0.188 r_chiral_restr 0.12 r_symmetry_nbtor_other 0.101 r_symmetry_xyhbond_nbd_other 0.095 r_bond_refined_d 0.016 r_gen_planes_refined 0.015 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2347 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling iMOSFLM data reduction PHASER phasing