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SARS-CoV-2 3CL Protease complexed with covalent inhibitor VK20
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9CEC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 100 mM sodium potassium tartrate, 10% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.29 46.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.922 α = 90 b = 64.058 β = 90.85 c = 103.116 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 PILATUS 6M 2022-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.979 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.38 37.85 96.1 0.035 14.9 7.2 120401 15.46
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.38 1.4 0.534
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 1.38 37.85 1.34 120368 2000 95.84 0.135 0.1343 0.1452 0.1778 0.179 20.65
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 14.2346 f_angle_d 1.0565 f_chiral_restr 0.0798 f_plane_restr 0.0142 f_bond_d 0.0082
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4716 Nucleic Acid Atoms Solvent Atoms 512 Heterogen Atoms 95
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing