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Crystal structure of the SARS-CoV-2 main protease in complex with INZ-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7C7P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1M MES pH5.0; 11% PEG 4000.
Crystal Properties Matthews coefficient Solvent content 2.71 54.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.236 α = 90 b = 82.9 β = 115.123 c = 51.489 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 PILATUS3 S 6M 2020-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.978531 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.73 19.44 97.2 0.057 0.019 0.999 21.6 10.1 37429
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.73 1.76 93.3 1.046 0.345 0.799 2.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7C7P 1.73 19.44 37425 1767 96.943 0.172 0.1701 0.1779 0.2092 0.2141 30.052
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] 1.255 -0.68 0.859 -1.025
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.383 r_dihedral_angle_other_3_deg 27.819 r_dihedral_angle_3_deg 14.955 r_dihedral_angle_4_deg 12.151 r_lrange_it 8.292 r_lrange_other 8.185 r_dihedral_angle_1_deg 7.144 r_scangle_it 6.004 r_scangle_other 6.002 r_mcangle_it 4.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.383 r_dihedral_angle_other_3_deg 27.819 r_dihedral_angle_3_deg 14.955 r_dihedral_angle_4_deg 12.151 r_lrange_it 8.292 r_lrange_other 8.185 r_dihedral_angle_1_deg 7.144 r_scangle_it 6.004 r_scangle_other 6.002 r_mcangle_it 4.328 r_mcangle_other 4.328 r_scbond_it 4 r_scbond_other 3.999 r_mcbond_it 3.206 r_mcbond_other 3.196 r_angle_refined_deg 1.867 r_angle_other_deg 1.509 r_symmetry_nbd_refined 0.223 r_nbd_refined 0.218 r_symmetry_xyhbond_nbd_refined 0.215 r_xyhbond_nbd_refined 0.201 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.176 r_nbd_other 0.166 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.086 r_symmetry_xyhbond_nbd_other 0.045 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2283 Nucleic Acid Atoms Solvent Atoms 313 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing