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SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-65
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 0.1M MIB buffer pH 6.5, 0.2 M (NH4)2SO4, 13-16% PEG 3350, 20% glycerol
Crystal Properties Matthews coefficient Solvent content 2.83 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.564 α = 90 b = 146.184 β = 99.53 c = 60.321 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) 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 2.9 48.73 98.1 0.293 0.164 0.956 4.7 3 17292
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.08 99.4 0.981 0.654 0.465 1.4 3.1
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 2.9 43.85 16373 892 98 0.2135 0.2094 0.2234 0.2929 0.2842 RANDOM 50.484
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] 2.48 3.72 -4.07 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.824 r_dihedral_angle_4_deg 18.129 r_dihedral_angle_3_deg 17.422 r_dihedral_angle_1_deg 7.335 r_angle_refined_deg 1.41 r_angle_other_deg 1.139 r_chiral_restr 0.05 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.824 r_dihedral_angle_4_deg 18.129 r_dihedral_angle_3_deg 17.422 r_dihedral_angle_1_deg 7.335 r_angle_refined_deg 1.41 r_angle_other_deg 1.139 r_chiral_restr 0.05 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 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 16 Heterogen Atoms 103
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing