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Crystal structure of SARS-CoV-2 Mpro-E166V mutant in complex with 13b-K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y2E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 0.2M Ammonium chloride, 0.1M Tris pH8.0, 20% w/vPEG 6000
Crystal Properties Matthews coefficient Solvent content 2.08 40.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.784 α = 90 b = 53.524 β = 99.906 c = 45.468 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 2022-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 44.83 98.8 0.997 5.4 3.5 13861
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 0.527
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 6y2e 2.2 44.83 13860 676 98.592 0.266 0.2612 0.264 0.3645 0.3674 51.706
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] 1.995 0.439 -0.686 -1.378
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.762 r_dihedral_angle_3_deg 18.563 r_dihedral_angle_4_deg 10.835 r_lrange_it 9.056 r_lrange_other 9.055 r_dihedral_angle_1_deg 8.494 r_mcangle_it 5.302 r_mcangle_other 5.302 r_scangle_it 4.645 r_scangle_other 4.643
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.762 r_dihedral_angle_3_deg 18.563 r_dihedral_angle_4_deg 10.835 r_lrange_it 9.056 r_lrange_other 9.055 r_dihedral_angle_1_deg 8.494 r_mcangle_it 5.302 r_mcangle_other 5.302 r_scangle_it 4.645 r_scangle_other 4.643 r_mcbond_other 3.322 r_mcbond_it 3.321 r_scbond_it 2.8 r_scbond_other 2.799 r_dihedral_angle_other_3_deg 1.63 r_angle_refined_deg 1.448 r_angle_other_deg 1.157 r_nbd_refined 0.227 r_symmetry_xyhbond_nbd_refined 0.208 r_symmetry_nbd_other 0.194 r_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.174 r_nbd_other 0.164 r_symmetry_nbd_refined 0.11 r_symmetry_nbtor_other 0.074 r_symmetry_xyhbond_nbd_other 0.07 r_chiral_restr 0.056 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2331 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing