☰ Navigation Tabs
The structure of the C117D variant of the COVID-2 main protease in complex with GC-376
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 298 0.1 M Bis-Tris (pH 6.5) and 12-20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.05 40.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.187 α = 90 b = 55.716 β = 100.9 c = 107.65 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 2.25 105.71 98.9 0.137 0.148 0.056 0.995 9.1 7 26022
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 2.25 2.29 99 1.198 1.304 0.507 0.572 6.6
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 2.25 105.71 1.34 25964 1259 98.69 0.1872 0.185 0.1849 0.2292 0.2307
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 15.501 f_angle_d 0.952 f_chiral_restr 0.053 f_bond_d 0.007 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4730 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 58
Software Software Software Name Purpose PHENIX refinement DIALS data scaling DIALS data reduction MOLREP phasing PDB_EXTRACT data extraction