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Crystal structure (monoclinic form) of the complex resulting from the reaction between SARS-CoV-2 (2019-nCoV) main protease and tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate (alpha-ketoamide 13b)
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 9 293 10% PEG 200, 0.1 M bis-tris propane, pH 9.0, 18% PEG 8,000
Crystal Properties Matthews coefficient Solvent content 2.75 55.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.085 α = 90 b = 80.926 β = 114.838 c = 51.659 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 2M 2020-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
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 1.95 43.369 100 0.076 0.083 0.032 0.999 15.5 6.8 26757
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 1.95 2.06 100 0.826 0.892 0.335 0.809 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2BX4 1.95 43.369 26755 1293 99.955 0.18 0.1779 0.187 0.2191 0.2206 4.83 36.377
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] 1.854 -0.302 1.848 -2.396
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.242 r_dihedral_angle_4_deg 17.946 r_dihedral_angle_3_deg 16.049 r_lrange_it 8.083 r_lrange_other 8.055 r_dihedral_angle_1_deg 7.221 r_scangle_it 6.008 r_scangle_other 6.007 r_mcangle_it 4.736 r_mcangle_other 4.735
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.242 r_dihedral_angle_4_deg 17.946 r_dihedral_angle_3_deg 16.049 r_lrange_it 8.083 r_lrange_other 8.055 r_dihedral_angle_1_deg 7.221 r_scangle_it 6.008 r_scangle_other 6.007 r_mcangle_it 4.736 r_mcangle_other 4.735 r_scbond_it 4.076 r_scbond_other 4.075 r_mcbond_other 3.252 r_mcbond_it 3.251 r_dihedral_angle_other_3_deg 1.836 r_angle_refined_deg 1.728 r_angle_other_deg 1.434 r_nbd_refined 0.205 r_symmetry_xyhbond_nbd_refined 0.198 r_xyhbond_nbd_refined 0.18 r_nbd_other 0.18 r_symmetry_nbd_other 0.177 r_nbtor_refined 0.175 r_symmetry_nbd_refined 0.147 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2341 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing