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Structure of SARS coronavirus main protease in complex with the alpha-ketoamide (S)-N-benzyl-3-((S)-2-cinnamamido-3-cyclopropylpropanamido)-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butanamide (Cinnamoyl-cyclopropylalanine-GlnLactam-CO-CO-NH-benzyl)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other SARS-CoV main protease
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 6 - 8% polyethylene glycol 6000, 0.1 M MES, pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.42 64.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.165 α = 90 b = 81.873 β = 104.34 c = 53.499 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 PILATUS 6M 2015-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 0.9919 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 43.83 98.3 0.06 0.039 0.997 10.5 3.3 30329
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 97.4 0.507 0.331 0.804 2.4 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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT SARS-CoV main protease 2 43.83 28787 1501 98.07 0.19512 0.19222 0.1989 0.25152 0.253 RANDOM 44.062
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] -2.71 1.59 1.34 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.724 r_dihedral_angle_4_deg 16.862 r_dihedral_angle_3_deg 16.138 r_long_range_B_refined 8.072 r_long_range_B_other 8.071 r_dihedral_angle_1_deg 7.345 r_scangle_other 6.635 r_mcangle_it 5.142 r_mcangle_other 5.141 r_scbond_it 4.625
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.724 r_dihedral_angle_4_deg 16.862 r_dihedral_angle_3_deg 16.138 r_long_range_B_refined 8.072 r_long_range_B_other 8.071 r_dihedral_angle_1_deg 7.345 r_scangle_other 6.635 r_mcangle_it 5.142 r_mcangle_other 5.141 r_scbond_it 4.625 r_scbond_other 4.623 r_mcbond_it 3.974 r_mcbond_other 3.97 r_angle_refined_deg 1.908 r_angle_other_deg 1.197 r_chiral_restr 0.137 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2371 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MOLREP phasing