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Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 21
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, 12.5 mM compound, 5% DMSO, 10% PEG300, 20% PEG3K, RT, 2 h.
Crystal Properties Matthews coefficient Solvent content 1.99 38.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.582 α = 90 b = 53.77 β = 100.526 c = 44.524 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 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 0.97625 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 1.63 56.33 98.1 0.06 0.074 0.043 0.998 11.1 5.1 32705
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 1.63 1.66 0.747 0.932 0.55 0.774 2 5.1
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 7B2J 1.63 43.813 32700 1621 98.027 0.192 0.1904 0.1896 0.2302 0.2287 Random selection 29.495
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] 3.13 0.059 -1.231 -1.797
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.217 r_dihedral_angle_3_deg 14.156 r_dihedral_angle_4_deg 9.985 r_dihedral_angle_1_deg 7.127 r_lrange_it 6.49 r_scangle_it 5.093 r_scbond_it 3.67 r_mcangle_it 3.224 r_mcbond_it 2.421 r_angle_refined_deg 1.552
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.217 r_dihedral_angle_3_deg 14.156 r_dihedral_angle_4_deg 9.985 r_dihedral_angle_1_deg 7.127 r_lrange_it 6.49 r_scangle_it 5.093 r_scbond_it 3.67 r_mcangle_it 3.224 r_mcbond_it 2.421 r_angle_refined_deg 1.552 r_nbtor_refined 0.321 r_nbd_refined 0.212 r_symmetry_nbd_refined 0.209 r_xyhbond_nbd_refined 0.159 r_symmetry_xyhbond_nbd_refined 0.125 r_chiral_restr 0.107 r_gen_planes_refined 0.01 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2358 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing