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Crystal structure of HCoV-229E 3CLpro with ALG-0987608 (inhibitor 1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YRZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 0.1 M Tris pH 8.0 and 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.38 48.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.287 α = 90 b = 76.374 β = 91.6 c = 77.013 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 9M 2024-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92019 NSLS-II 17-ID-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 1.41 34.37 99.8 0.127 0.138 0.052 0.998 7.9 6.9 118296
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 1.41 1.49 98.8 1.26 1.385 0.569 0.447 5.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.41 34.37 1.34 118225 5827 99.79 0.1942 0.1931 0.1936 0.2169 0.2168
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 15.974 f_angle_d 0.967 f_chiral_restr 0.093 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4618 Nucleic Acid Atoms Solvent Atoms 548 Heterogen Atoms 115
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing PHASER phasing PDB_EXTRACT data extraction