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Crystal structure of SARS-CoV-2 main protease in complex with Z-IETD-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 0.1 M MES monohydrate pH 6.0, 20% w/v Polyethylene glycol monomethyl ether 2,000
Crystal Properties Matthews coefficient Solvent content 2.01 38.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.387 α = 90 b = 55.248 β = 101.516 c = 46.901 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 2020-07-25 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 2.054 30 99.5 0.059 20.47 3.6 17239
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 2.054 2.13 98.7 0.494 2.3 3.3
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 6Y2E, 6LU7 2.054 21.594 16657 835 95.79 0.212 0.2097 0.2463 0.2425 28.341
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] -0.241 -0.314 0.442 -0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.602 r_dihedral_angle_other_3_deg 20.701 r_dihedral_angle_3_deg 15.877 r_dihedral_angle_4_deg 15.673 r_dihedral_angle_1_deg 8.253 r_lrange_it 6.54 r_lrange_other 6.484 r_scangle_it 4.569 r_scangle_other 4.468 r_mcangle_it 3.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.602 r_dihedral_angle_other_3_deg 20.701 r_dihedral_angle_3_deg 15.877 r_dihedral_angle_4_deg 15.673 r_dihedral_angle_1_deg 8.253 r_lrange_it 6.54 r_lrange_other 6.484 r_scangle_it 4.569 r_scangle_other 4.468 r_mcangle_it 3.727 r_mcangle_other 3.727 r_scbond_it 2.939 r_scbond_other 2.861 r_mcbond_it 2.482 r_mcbond_other 2.478 r_angle_refined_deg 1.37 r_angle_other_deg 1.3 r_nbd_other 0.238 r_nbd_refined 0.226 r_symmetry_nbd_other 0.205 r_symmetry_nbd_refined 0.188 r_nbtor_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.176 r_xyhbond_nbd_refined 0.164 r_symmetry_xyhbond_nbd_other 0.116 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2374 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing