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Structure of SARS-CoV-2 Papain-like protease PLpro in complex with 3, 4-Dihydroxybenzoic acid, methyl ester
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NFV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 Co-crystallization with the compounds was achieved mixing 0.2 uL of protein solution (22 mg/mL) in 50 mM TRIS buffer (pH 8.0) containing 1 mM TCEP and 150 mM NaCl with 0.1 uL of reservoir solution consisting of 1.0M NaH2PO4/1.0MKH2PO4, 100mM Tris_HCl pH=7.5. This growth solution was equilibrated by sitting drop vapor diffusion against 80 uL reservoir solution. Prior to crystallization 100 nL droplets of 10 mM compound solutions in DMSO were applied to the wells of SwissCI 96-well plates (2-well) and subsequently dried in vacuum.
Crystal Properties Matthews coefficient Solvent content 3.68 66.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.391 α = 90 b = 82.391 β = 90 c = 134.132 γ = 120
Symmetry Space Group P 32 2 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 PILATUS 6M 2020-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.72 48.92 99.954 1 16.66 10.6 56596
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 1.72 1.782 0.576 10.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7nfv 1.72 48.868 56588 2834 99.954 0.176 0.1749 0.1835 0.202 0.2065 33.774
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] -0.073 -0.037 -0.073 0.238
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.102 r_dihedral_angle_4_deg 17.491 r_dihedral_angle_3_deg 15.352 r_lrange_it 7.346 r_lrange_other 7.092 r_dihedral_angle_1_deg 6.36 r_scangle_it 5.45 r_scangle_other 5.365 r_scbond_it 3.708 r_scbond_other 3.564
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.102 r_dihedral_angle_4_deg 17.491 r_dihedral_angle_3_deg 15.352 r_lrange_it 7.346 r_lrange_other 7.092 r_dihedral_angle_1_deg 6.36 r_scangle_it 5.45 r_scangle_other 5.365 r_scbond_it 3.708 r_scbond_other 3.564 r_mcangle_it 2.815 r_mcangle_other 2.814 r_mcbond_it 2.125 r_mcbond_other 2.1 r_angle_refined_deg 1.933 r_angle_other_deg 1.534 r_symmetry_nbd_refined 0.253 r_nbd_other 0.221 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.212 r_nbtor_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.178 r_symmetry_nbd_other 0.177 r_symmetry_xyhbond_nbd_other 0.13 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2502 Nucleic Acid Atoms Solvent Atoms 330 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing