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Crystal structure (orthorhombic 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 2BX4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M Carboxylic acids (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M sodium citrate tribasic dihydrate, 0.2 M potassium sodium tartrate tetrahydrate, 0.2 M sodium oxamate), 0.1 M buffer system 3 (1.0 M tris (base), bicine, pH 8.5), pH 8.5, 30% precipitant mix 1 (20% v/v PEG 500 methyl ether, 10% PEG 20,000))
Crystal Properties Matthews coefficient Solvent content 2.67 53.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.566 α = 90 b = 101.602 β = 90 c = 103.696 γ = 90
Symmetry Space Group P 21 21 21
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 2.2 49.84 100 0.17 0.177 0.048 0.998 13.1 13.1 37519 35.58
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 100 0.414 0.662 2.1 12.1
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 2.2 41.355 37448 1761 99.947 0.191 0.189 0.1958 0.2343 0.1935 5.07 41.09
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] -0.015 -0.076 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.326 r_dihedral_angle_6_deg 15.862 r_lrange_other 9.93 r_lrange_it 9.928 r_dihedral_angle_1_deg 7.738 r_dihedral_angle_2_deg 7.719 r_scangle_it 7.495 r_scangle_other 7.494 r_mcangle_it 6.492 r_mcangle_other 6.492
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.326 r_dihedral_angle_6_deg 15.862 r_lrange_other 9.93 r_lrange_it 9.928 r_dihedral_angle_1_deg 7.738 r_dihedral_angle_2_deg 7.719 r_scangle_it 7.495 r_scangle_other 7.494 r_mcangle_it 6.492 r_mcangle_other 6.492 r_scbond_it 4.985 r_scbond_other 4.984 r_mcbond_it 4.432 r_mcbond_other 4.431 r_angle_refined_deg 1.62 r_angle_other_deg 0.759 r_dihedral_angle_other_3_deg 0.64 r_nbd_refined 0.22 r_symmetry_nbd_other 0.202 r_symmetry_nbd_refined 0.189 r_symmetry_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.183 r_nbd_other 0.17 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.085 r_symmetry_xyhbond_nbd_other 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4669 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing