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SARS-CoV-2 Main Protease with Secutrelvir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9D08
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 19% PEG Smear Medium, 0.1 M MES
Crystal Properties Matthews coefficient Solvent content 2.8 56.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.913 α = 90 b = 82.507 β = 115.331 c = 51.658 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 9M 2026-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.587 60.348 96.5 0.079 0.998 8.8 6.6 48423 27.91
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 1.587 1.614 100 3.535 3.831 1.461 0.327 0.6 6.8
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 1.59 46.69 1.35 47455 2293 94.58 0.196 0.1949 0.1945 0.2192 0.218 39.99
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 18.6408 f_angle_d 0.9963 f_chiral_restr 0.0506 f_plane_restr 0.0075 f_bond_d 0.0072
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2333 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 39
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing