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SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-83
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JRN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 0.1 M MIB buffer pH 6.5, 0.2M (NH4)2SO4, 13-16% PEG 3350, 20% glycerol
Crystal Properties Matthews coefficient Solvent content 2.81 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.713 α = 90 b = 147.365 β = 99.72 c = 60.277 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 9M 2020-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.1271 APS 21-ID-D
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 2.3 46.29 95.1 0.164 0.196 0.106 0.988 5 3.3 33851
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 76.1 0.148 0.5 2.3
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 7JRN 2.3 46.29 32102 1723 94.98 0.2196 0.2174 0.2238 0.2598 0.2591 RANDOM 52.873
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] 1.63 1.02 0.03 -1.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.758 r_dihedral_angle_3_deg 16.844 r_dihedral_angle_4_deg 16.284 r_dihedral_angle_1_deg 6.291 r_angle_refined_deg 1.322 r_angle_other_deg 1.119 r_chiral_restr 0.047 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.758 r_dihedral_angle_3_deg 16.844 r_dihedral_angle_4_deg 16.284 r_dihedral_angle_1_deg 6.291 r_angle_refined_deg 1.322 r_angle_other_deg 1.119 r_chiral_restr 0.047 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5014 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 118
Software Software Software Name Purpose XDS data reduction XSCALE data scaling Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction