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SARS-CoV-2 Main Protease in complex with (1R)-3-oxo-N-[2-oxo-2-(N-phenylanilino)ethyl]indane-1-carboxamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NTT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 0.2M Calcium Chloride, 0.1 Hepes pH7.5, 30% (w/v) PEG4000
Cryo-protection with glycerol (10%)
Crystal Properties Matthews coefficient Solvent content 2.13 42.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.321 α = 90 b = 124.244 β = 101.015 c = 71.227 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 2023-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9801 SOLEIL PROXIMA 1
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 1.77 46.482 97.7 0.099 0.117 0.061 0.998 10.6 7.2 107302
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 1.77 1.8 1.371 1.617 0.848 0.663 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.77 46.482 107268 5408 97.564 0.17 0.1673 0.1668 0.214 0.2148 25.864
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] 1.149 0.236 -2.074 0.775
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.519 r_dihedral_angle_6_deg 15.376 r_dihedral_angle_3_deg 14.555 r_lrange_other 8.22 r_lrange_it 8.218 r_scangle_it 7.324 r_scangle_other 7.323 r_dihedral_angle_1_deg 7.21 r_scbond_it 5.163 r_scbond_other 5.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.519 r_dihedral_angle_6_deg 15.376 r_dihedral_angle_3_deg 14.555 r_lrange_other 8.22 r_lrange_it 8.218 r_scangle_it 7.324 r_scangle_other 7.323 r_dihedral_angle_1_deg 7.21 r_scbond_it 5.163 r_scbond_other 5.163 r_dihedral_angle_other_2_deg 4.207 r_mcangle_it 4.194 r_mcangle_other 4.194 r_mcbond_it 3.292 r_mcbond_other 3.289 r_angle_refined_deg 2.378 r_angle_other_deg 0.795 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.213 r_symmetry_nbd_other 0.199 r_symmetry_xyhbond_nbd_refined 0.199 r_nbtor_refined 0.191 r_symmetry_nbd_refined 0.183 r_nbd_other 0.171 r_symmetry_xyhbond_nbd_other 0.151 r_chiral_restr 0.117 r_symmetry_nbtor_other 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.014 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9380 Nucleic Acid Atoms Solvent Atoms 784 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing MxCuBE data collection XDS data reduction