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Crystal structure of SARS-CoV-2 papain-like protease (Cys111Ser) in complex with YL1004
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YBG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 6% (w/v) PEG8000, 100 mM MES/Sodium hydroxide pH 6.0, 200 mM zinc acetate and 20% PEG400
Crystal Properties Matthews coefficient Solvent content 4.85 74.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.639 α = 90 b = 111.639 β = 90 c = 220.006 γ = 90
Symmetry Space Group I 41 2 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 PILATUS 6M 2025-01-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97861 SSRF BL19U1
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 2.7 99.56 95.9 0.511 0.521 0.103 0.993 10.1 24.9 18747
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 2.7 2.83 100 1.902 1.941 0.386 0.432 1.9
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 THROUGHOUT 2.7 64.14 1.33 18629 956 95.36 0.2044 0.2029 0.2178 0.2313 0.2421
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 15.468 f_angle_d 1.208 f_chiral_restr 0.059 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2435 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 60
Software Software Software Name Purpose PHENIX refinement MOLREP phasing Aimless data scaling XDS data reduction