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Structure of PEDV main protease bound to potent broad-spectrum non-covalent inhibitor X77
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HYO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 293 PEDV-3CLpro:77 inhibitor complex was co-crystallized by setting up 2 uL drops that were composed of 1 uL of purified PEDV-3CLpro (2.4 mg/mL) that had been incubated for three hours with a 3 molar excess of compound 77, and 1 uL of reservoir solution: 0.20 M malonic acid (MIB) pH 4.0 and 25% PEG-3350
Crystal Properties Matthews coefficient Solvent content 2.11 41.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.679 α = 90 b = 85.257 β = 100.46 c = 58.186 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 CCD MARMOSAIC 300 mm CCD 2020-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.988 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 1.55 50 97.8 0.086 0.04 28.9 4.8 76919 20.34
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 79.2 0.739 0.469 0.637 1.35 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5HYO 1.55 27.87 1.34 76888 1998 97.42 0.1768 0.1758 0.1761 0.2136 0.2142 34.69
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.7667 f_angle_d 0.8409 f_chiral_restr 0.0519 f_bond_d 0.0058 f_plane_restr 0.0045
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4590 Nucleic Acid Atoms Solvent Atoms 534 Heterogen Atoms 75
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing