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SARS-CoV-2 Main Protease complexed with (1R)-N-(3-chlorophenyl)-3-oxo-indane-1-carboxamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7K3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.2M NaFORMATE, 20% PEG 3350
then soaking with inhibitor (in DSMO) and cryoprotected with 10% glycerol
Crystal Properties Matthews coefficient Solvent content 2 38.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.95 α = 90 b = 53.6 β = 100.94 c = 44.62 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 9M 2022-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.91840 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.795 48.464 99.4 0.069 0.999 25.02 6.7 24927 19.85
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.795 1.9 0.276 0.98 7.81
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 1.795 48.464 24927 1247 99.497 0.161 0.1579 0.1575 0.2109 0.2101 19.789
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] 1.328 0.018 -0.194 -1.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.226 r_dihedral_angle_2_deg 14.327 r_dihedral_angle_3_deg 13.966 r_dihedral_angle_1_deg 7.18 r_lrange_it 5.624 r_lrange_other 5.515 r_scangle_it 4.13 r_scangle_other 4.129 r_scbond_it 2.805 r_scbond_other 2.804
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.226 r_dihedral_angle_2_deg 14.327 r_dihedral_angle_3_deg 13.966 r_dihedral_angle_1_deg 7.18 r_lrange_it 5.624 r_lrange_other 5.515 r_scangle_it 4.13 r_scangle_other 4.129 r_scbond_it 2.805 r_scbond_other 2.804 r_mcangle_it 2.531 r_mcangle_other 2.53 r_mcbond_it 1.833 r_mcbond_other 1.825 r_angle_refined_deg 1.538 r_angle_other_deg 0.516 r_nbd_refined 0.222 r_symmetry_xyhbond_nbd_refined 0.208 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.179 r_symmetry_nbd_refined 0.16 r_nbd_other 0.149 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.075 r_gen_planes_refined 0.009 r_bond_refined_d 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 2347 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement MOLREP phasing XDS data reduction Aimless data scaling MxCuBE data collection