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The crystal structure of wild-type Papain-Like Protease of SARS-CoV-2 with TDI-015937-NX-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WRH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.05 M Ammonium sulfate, 0.1 M Sodium citrate (No pH), and 15% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.56 56.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.755 α = 90 b = 146.045 β = 99.077 c = 60.149 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 EIGER X 16M 2023-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.97857 SSRF BL10U2
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 2.56 73.02 99.1 0.176 0.213 0.086 0.973 7.2 6.2 25404
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 2.56 2.67 98.2 0.727 0.932 0.571 0.612 2 4.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.56 73.02 25367 1271 98.939 0.22 0.22039 0.2173 0.2223 0.278 0.2743 RANDOM 24.887
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] 1.178 0.87 1.513 -2.824
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.511 r_dihedral_angle_2_deg 11.831 r_dihedral_angle_3_deg 11.399 r_dihedral_angle_1_deg 5.652 r_lrange_it 2.928 r_lrange_other 2.915 r_mcangle_it 1.445 r_mcangle_other 1.445 r_scangle_it 0.987 r_scangle_other 0.987
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.511 r_dihedral_angle_2_deg 11.831 r_dihedral_angle_3_deg 11.399 r_dihedral_angle_1_deg 5.652 r_lrange_it 2.928 r_lrange_other 2.915 r_mcangle_it 1.445 r_mcangle_other 1.445 r_scangle_it 0.987 r_scangle_other 0.987 r_angle_refined_deg 0.802 r_mcbond_it 0.78 r_mcbond_other 0.779 r_angle_other_deg 0.625 r_scbond_it 0.513 r_scbond_other 0.513 r_symmetry_nbd_other 0.2 r_nbd_other 0.191 r_nbd_refined 0.181 r_nbtor_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.17 r_metal_ion_refined 0.164 r_xyhbond_nbd_refined 0.117 r_symmetry_nbd_refined 0.086 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.034 r_gen_planes_other 0.004 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5014 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 85
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PHASER phasing Coot model building