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Crystal structure of the complex resulting from the reaction between the SARS-CoV main protease and tert-butyl (1-((S)-3-cyclohexyl-1-(((S)-4-(cyclopropylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BX4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.1 MES, 6% PEG 6,000, pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.37 63.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.905 α = 90 b = 82.247 β = 104.465 c = 53.131 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 PIXEL DECTRIS PILATUS3 S 6M 2019-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0000 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.9 43.67 99.4 0.048 0.056 0.028 0.998 12.8 3.9 35225
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 99.1 0.639 0.742 0.372 0.88 2.2 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 2BX4 1.9 42.356 35112 1700 98.993 0.209 0.2062 0.2128 0.2576 0.2587 48.235
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] -2.775 1.733 1.732 0.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.941 r_dihedral_angle_4_deg 18.135 r_dihedral_angle_3_deg 15.721 r_lrange_it 9.061 r_lrange_other 9.027 r_dihedral_angle_1_deg 7.877 r_scangle_it 6.9 r_scangle_other 6.898 r_mcangle_it 5.865 r_mcangle_other 5.865
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.941 r_dihedral_angle_4_deg 18.135 r_dihedral_angle_3_deg 15.721 r_lrange_it 9.061 r_lrange_other 9.027 r_dihedral_angle_1_deg 7.877 r_scangle_it 6.9 r_scangle_other 6.898 r_mcangle_it 5.865 r_mcangle_other 5.865 r_scbond_it 4.857 r_scbond_other 4.857 r_mcbond_it 4.333 r_mcbond_other 4.33 r_angle_refined_deg 1.822 r_angle_other_deg 1.45 r_dihedral_angle_other_3_deg 0.321 r_nbd_refined 0.214 r_nbd_other 0.197 r_xyhbond_nbd_refined 0.19 r_symmetry_nbd_other 0.189 r_symmetry_xyhbond_nbd_refined 0.184 r_chiral_restr 0.179 r_nbtor_refined 0.176 r_symmetry_nbd_refined 0.157 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2371 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing