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wild-type SARS-CoV-2 main protease in complex with MG-132
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LU7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Tris pH 8.5, 0.2 M sodium chloride, 25% w/v PEG3,350
Crystal Properties Matthews coefficient Solvent content 2.08 40.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.978 α = 90 b = 55.14 β = 102.34 c = 47.111 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 CCD RAYONIX MX300HE 2020-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 0.99984 NSRRC BL15A1
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 2.145 50 98.2 0.046 28.582 4.2 15052
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 2.145 2.23 95.5 0.338 3.638 3.8
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 6LU7, 6Y2E 2.15 27.65 14053 739 96.28 0.23118 0.22811 0.2311 0.28918 0.2939 RANDOM 28.398
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] -0.13 -0.25 0.29 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.126 r_dihedral_angle_3_deg 17.238 r_dihedral_angle_4_deg 12.83 r_dihedral_angle_1_deg 9.079 r_long_range_B_other 5.996 r_long_range_B_refined 5.959 r_mcangle_it 3.582 r_mcangle_other 3.581 r_scangle_other 3.45 r_mcbond_it 2.208
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.126 r_dihedral_angle_3_deg 17.238 r_dihedral_angle_4_deg 12.83 r_dihedral_angle_1_deg 9.079 r_long_range_B_other 5.996 r_long_range_B_refined 5.959 r_mcangle_it 3.582 r_mcangle_other 3.581 r_scangle_other 3.45 r_mcbond_it 2.208 r_mcbond_other 2.206 r_scbond_other 2.183 r_scbond_it 2.147 r_angle_refined_deg 1.737 r_angle_other_deg 1.225 r_chiral_restr 0.056 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2323 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing