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Crystal Structure of the SARS-CoV-2 (COVID-19) main protease with inhibitor AD06cn
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 0.1 M Bis-Tris pH6.5, 30% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.7 54.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.62 α = 90 b = 80.47 β = 97.168 c = 89.147 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 2025-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
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 1.97 29.09 99 0.153 0.189 0.109 0.964 4.9 2.9 25381
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 2.2 2.27 99.1 0.369 2.9
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 1.97 24.288 25381 1242 98.548 0.219 0.2162 0.2146 0.2653 0.2577 26.881
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] -1.291 0.126 0.724 0.519
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.65 r_dihedral_angle_6_deg 14.072 r_dihedral_angle_2_deg 10.778 r_lrange_it 9.659 r_lrange_other 9.53 r_dihedral_angle_1_deg 7.62 r_scangle_it 5.851 r_scangle_other 5.85 r_mcangle_it 3.942 r_mcangle_other 3.942
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.65 r_dihedral_angle_6_deg 14.072 r_dihedral_angle_2_deg 10.778 r_lrange_it 9.659 r_lrange_other 9.53 r_dihedral_angle_1_deg 7.62 r_scangle_it 5.851 r_scangle_other 5.85 r_mcangle_it 3.942 r_mcangle_other 3.942 r_scbond_it 3.646 r_scbond_other 3.631 r_mcbond_it 2.506 r_mcbond_other 2.503 r_angle_refined_deg 1.833 r_angle_other_deg 0.609 r_xyhbond_nbd_refined 0.28 r_symmetry_xyhbond_nbd_refined 0.271 r_nbd_refined 0.222 r_symmetry_nbd_other 0.204 r_nbd_other 0.202 r_nbtor_refined 0.189 r_symmetry_nbd_refined 0.127 r_symmetry_xyhbond_nbd_other 0.118 r_symmetry_nbtor_other 0.091 r_chiral_restr 0.085 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 2323 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling iMOSFLM data reduction PHASER phasing