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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Q192T Mutant in Complex with Inhibitor GC376
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7LYH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 25% PEG 3350, 0.1M Potassium/Sodium Tartrate, 0.005M Magnesium Chloride
Crystal Properties Matthews coefficient Solvent content 1.99 38.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.03 α = 67 b = 53.241 β = 79.57 c = 59.532 γ = 88.8
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300-HS 2022-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.87 50 93.5 0.079 9.03 2.2 10878
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.87 2.92 0.192 3.06
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 (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 THROUGHOUT 7LYH 2.87 48.98 10160 512 89.62 0.2294 0.2271 0.2272 0.2722 0.2694 RANDOM 54.062
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] -1.18 0.89 -0.33 -0.74 -1.31 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.771 r_dihedral_angle_1_deg 5.994 r_dihedral_angle_2_deg 2.23 r_angle_refined_deg 1.204 r_angle_other_deg 0.854 r_chiral_restr 0.055 r_bond_other_d 0.043 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4690 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing