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The crystal structure of SARS-CoV-2 Main Protease in complex with masitinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JFQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 296 0.2 M NaCl,
0.1 M MES,
20% (w/v) PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.79 55.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.591 α = 90 b = 81.299 β = 114.62 c = 51.859 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 Mirror 2020-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9791 APS 19-ID
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 1.6 43.5 98.5 0.084 0.098 0.05 0.999 26.3 3.5 48121 -3 23.98
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 1.6 1.63 95.4 0.877 1.111 0.672 0.354 1.1 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 7JFQ 1.6 43.5 1.35 47565 2338 97.1 0.1698 0.1686 0.1695 0.1918 0.1942 random 33.49
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.5532 f_angle_d 1.4285 f_chiral_restr 0.096 f_bond_d 0.0156 f_plane_restr 0.0093
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2334 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing