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SARS-CoV-2 Main Protease in complex with (3S)-3-[(3R)-3-phenylpiperidine-1-carbonyl]indan-1-one
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 7.5 293 0.2 M sodium formate, 20% PEG 3350. Then soaking with inhibitor (DMSO) and cryo-protection with glycerol (10%).
Crystal Properties Matthews coefficient Solvent content 1.99 38.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.64 α = 90 b = 53.58 β = 102.72 c = 44.83 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 0.9184 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.794 48.367 99.3 0.076 0.082 0.999 13.3 6.8 24802 31.62
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.794 1.84 93.6 1.036 1.126 0.626 1.5
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 1.794 48.367 24801 1240 99.403 0.172 0.1693 0.1682 0.2287 0.2262 35.277
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] 1.362 0.779 -1.296 -0.379
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.408 r_dihedral_angle_2_deg 13.445 r_dihedral_angle_3_deg 12.842 r_lrange_it 7.67 r_lrange_other 7.655 r_dihedral_angle_1_deg 7.593 r_scangle_it 6.716 r_scangle_other 6.715 r_scbond_it 4.814 r_scbond_other 4.802
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.408 r_dihedral_angle_2_deg 13.445 r_dihedral_angle_3_deg 12.842 r_lrange_it 7.67 r_lrange_other 7.655 r_dihedral_angle_1_deg 7.593 r_scangle_it 6.716 r_scangle_other 6.715 r_scbond_it 4.814 r_scbond_other 4.802 r_mcangle_it 3.832 r_mcangle_other 3.831 r_mcbond_other 2.965 r_mcbond_it 2.963 r_angle_refined_deg 2.427 r_angle_other_deg 0.852 r_symmetry_nbd_refined 0.225 r_nbd_refined 0.215 r_symmetry_nbd_other 0.199 r_xyhbond_nbd_refined 0.195 r_nbtor_refined 0.192 r_symmetry_xyhbond_nbd_refined 0.172 r_nbd_other 0.154 r_chiral_restr 0.138 r_symmetry_nbtor_other 0.091 r_symmetry_xyhbond_nbd_other 0.018 r_bond_refined_d 0.016 r_gen_planes_refined 0.015 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2348 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MxCuBE data collection MOLREP phasing