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The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with human ISG15
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YVA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 0.02 M MgCl2, 0.1 M HEPES buffer, 22% poly(acrylicacid sodium salt) 5100
Crystal Properties Matthews coefficient Solvent content 3.71 66.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.673 α = 90 b = 220.87 β = 90 c = 232.787 γ = 90
Symmetry Space Group C 2 2 21
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 PILATUS3 X 6M 2021-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID
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 2.98 48.99 99.9 0.214 0.232 0.089 0.985 5.3 6.7 78254
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 3.03 3.08 100 2.18 2.361 0.9 0.364 1.23 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6YVA 2.98 48.99 74428 3786 97.15 0.1971 0.1951 0.1948 0.2358 0.2317 RANDOM 76.102
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] 2.35 -1.64 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.302 r_dihedral_angle_4_deg 20.053 r_dihedral_angle_3_deg 16.544 r_dihedral_angle_1_deg 6.51 r_angle_refined_deg 1.283 r_angle_other_deg 1.089 r_chiral_restr 0.042 r_bond_refined_d 0.004 r_bond_other_d 0.003 r_gen_planes_refined 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.302 r_dihedral_angle_4_deg 20.053 r_dihedral_angle_3_deg 16.544 r_dihedral_angle_1_deg 6.51 r_angle_refined_deg 1.283 r_angle_other_deg 1.089 r_chiral_restr 0.042 r_bond_refined_d 0.004 r_bond_other_d 0.003 r_gen_planes_refined 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18418 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 5
Software Software Software Name Purpose HKL-3000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 phasing