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Crystal structure of SARS-CoV-2 main protease in complex with Z-DEVD-FMK
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y2E 6Y2E, 6LU7 experimental model PDB 6LU7 6Y2E, 6LU7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.15 M DL-Malic acid pH 7.0, 20% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 1.96 37.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.178 α = 90 b = 54.636 β = 101.134 c = 45.279 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 1.00000 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 2.2 30 98.83 0.067 19.69 3.8 13674
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 2.2 2.28 95.43 0.35 3.73 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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6Y2E, 6LU7 2.2 27.532 13639 664 98.805 0.18 0.1782 0.1871 0.2221 0.1872 31.689
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] -0.197 -0.403 0.114 0.225
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.466 r_dihedral_angle_4_deg 18.568 r_dihedral_angle_3_deg 16.387 r_dihedral_angle_1_deg 8.21 r_lrange_it 7.791 r_lrange_other 7.563 r_scangle_it 5.268 r_scangle_other 5.147 r_dihedral_angle_other_3_deg 4.314 r_mcangle_it 4.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.466 r_dihedral_angle_4_deg 18.568 r_dihedral_angle_3_deg 16.387 r_dihedral_angle_1_deg 8.21 r_lrange_it 7.791 r_lrange_other 7.563 r_scangle_it 5.268 r_scangle_other 5.147 r_dihedral_angle_other_3_deg 4.314 r_mcangle_it 4.131 r_mcangle_other 4.131 r_scbond_it 3.511 r_scbond_other 3.399 r_mcbond_it 2.646 r_mcbond_other 2.643 r_angle_refined_deg 1.429 r_angle_other_deg 1.329 r_symmetry_xyhbond_nbd_refined 0.26 r_nbd_refined 0.205 r_symmetry_nbd_other 0.196 r_nbd_other 0.193 r_nbtor_refined 0.173 r_symmetry_nbd_refined 0.169 r_xyhbond_nbd_refined 0.135 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.068 r_symmetry_xyhbond_nbd_other 0.044 r_bond_refined_d 0.009 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 2369 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing