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Crystal structure of SARS-CoV-2 main protease in complex with Tafenoquine
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 Ammonium acetate,0.1 M BIS-TRIS pH 5.5, 17% w/v Polyethylene glycol 10000
Crystal Properties Matthews coefficient Solvent content 1.99 38.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.294 α = 90 b = 54.675 β = 100.861 c = 44.79 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 2020-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 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 2.175 27.586 99.62 0.047 27.382 3.7 14115
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 2.175 2.253 0.234 3.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6LU7 2.175 27.586 14115 708 99.626 0.184 0.1812 0.2338 0.2359 30.516
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] -0.028 -0.304 -0.032 0.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.056 r_dihedral_angle_3_deg 15.514 r_dihedral_angle_4_deg 15.186 r_lrange_it 8.281 r_dihedral_angle_1_deg 7.933 r_lrange_other 7.374 r_scangle_it 5.412 r_scangle_other 4.923 r_mcangle_it 3.666 r_mcangle_other 3.665
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.056 r_dihedral_angle_3_deg 15.514 r_dihedral_angle_4_deg 15.186 r_lrange_it 8.281 r_dihedral_angle_1_deg 7.933 r_lrange_other 7.374 r_scangle_it 5.412 r_scangle_other 4.923 r_mcangle_it 3.666 r_mcangle_other 3.665 r_scbond_it 3.562 r_scbond_other 3.281 r_mcbond_it 2.454 r_mcbond_other 2.451 r_angle_refined_deg 1.38 r_angle_other_deg 1.333 r_symmetry_xyhbond_nbd_refined 0.304 r_nbd_other 0.277 r_nbd_refined 0.23 r_symmetry_nbd_refined 0.205 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.155 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.068 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2329 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing