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The structure of the C117D variant of the COVID-2 main protease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.1 M Bis-Tris (pH 6.5) and 12-20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.97 37.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.558 α = 90 b = 62.239 β = 101.64 c = 63.21 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 EIGER2 S 16M 2025-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE 7B2 0.9686 CHESS 7B2
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 2.05 62.2 100 0.147 0.159 0.06 0.997 19.8 6.9 16592 25.75
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 2.05 2.09 100 1.232 1.33 0.498 0.956 5.2
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.05 62.2 1.46 16572 814 99.97 0.1823 0.1802 0.1802 0.2238 0.2239 random
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 15.791 f_angle_d 0.848 f_chiral_restr 0.051 f_bond_d 0.007 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2276 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction DIALS data reduction DIALS data scaling MOLREP phasing