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SARS-CoV-2 3CL protease (3CLpro) in complex with compound 6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M2N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 2-8% PEG6000, 100 mM MES, pH 6.0-7.25, 3% DMSO
Crystal Properties Matthews coefficient Solvent content 2.25 45.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.494 α = 90 b = 63.433 β = 90 c = 105.604 γ = 90
Symmetry Space Group P 21 21 2
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 9M 2024-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
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 1.49 54.38 100 0.096 0.101 0.028 0.999 13.7 12.5 50327
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 1.49 1.58 99.8 2.467 2.608 0.833 0.459 9.4
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 6M2N 1.49 41.78 1.34 50105 2467 99.58 0.1979 0.1962 0.1966 0.2301 0.2303
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 9.972 f_angle_d 1.331 f_chiral_restr 0.106 f_plane_restr 0.013 f_bond_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2326 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 31
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing