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Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 15
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7B2J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.75 293 100 nL protein (8.3 mg/mL, 50 mM Tris pH 8.0, 300 mM NaCl), 50 nL seeds, 450 nL reservoir (200 mM HEPES pH 7.75, 5% DMSO, 12.5% PEG4K).
Soaking: 200 mM HEPES pH 7.75, 12 mM compound, 5% DMSO, 10% PEG300, 20% PEG3K, RT, 2 h.
Crystal Properties Matthews coefficient Solvent content 2.01 38.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.572 α = 90 b = 53.822 β = 100.492 c = 114.768 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 16M 2020-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.976 MAX IV BioMAX
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 1.64 48.67 99.9 0.065 0.079 0.045 0.998 11.3 5.6 65712
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 1.64 1.67 100 0.431 0.529 0.302 0.94 3.2 5.6
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 7B2J 1.64 48.627 65694 3193 99.919 0.203 0.2012 0.2094 0.2387 0.2433 18.668
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] -0.87 -0.586 -0.339 1.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.721 r_dihedral_angle_3_deg 12.878 r_dihedral_angle_4_deg 12.715 r_dihedral_angle_1_deg 7.291 r_lrange_it 5.518 r_lrange_other 5.483 r_scangle_it 3.954 r_scangle_other 3.954 r_scbond_it 2.634 r_scbond_other 2.633
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.721 r_dihedral_angle_3_deg 12.878 r_dihedral_angle_4_deg 12.715 r_dihedral_angle_1_deg 7.291 r_lrange_it 5.518 r_lrange_other 5.483 r_scangle_it 3.954 r_scangle_other 3.954 r_scbond_it 2.634 r_scbond_other 2.633 r_mcangle_it 2.544 r_mcangle_other 2.543 r_mcbond_it 1.767 r_mcbond_other 1.767 r_angle_refined_deg 1.704 r_angle_other_deg 1.507 r_nbd_other 0.215 r_symmetry_xyhbond_nbd_refined 0.214 r_nbd_refined 0.208 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.168 r_symmetry_nbd_refined 0.103 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4716 Nucleic Acid Atoms Solvent Atoms 492 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing