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Structure of SARS-CoV-2 Papain-like protease PLpro
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 277 1.0M NaH2PO4/1.0MKH2PO4
100mM Tris_HCl pH=7.5
Crystal Properties Matthews coefficient Solvent content 3.68 66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.33 α = 90 b = 82.33 β = 90 c = 134.32 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 2020-12-19 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 1.42 48.89 100 0.97 28.3 52.9 99793
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 1.42 1.44 0.36
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 7jrn 1.42 48.89 99791 4919 99.989 0.155 0.1538 0.1602 0.1714 0.1749 31.543
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] 0.299 0.15 0.299 -0.972
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.599 r_dihedral_angle_3_deg 14.271 r_dihedral_angle_4_deg 12.021 r_lrange_it 7.261 r_lrange_other 6.907 r_dihedral_angle_1_deg 6.089 r_scangle_it 5.636 r_scangle_other 5.631 r_scbond_it 3.892 r_scbond_other 3.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.599 r_dihedral_angle_3_deg 14.271 r_dihedral_angle_4_deg 12.021 r_lrange_it 7.261 r_lrange_other 6.907 r_dihedral_angle_1_deg 6.089 r_scangle_it 5.636 r_scangle_other 5.631 r_scbond_it 3.892 r_scbond_other 3.89 r_mcangle_it 2.607 r_mcangle_other 2.606 r_angle_refined_deg 2.308 r_mcbond_it 1.94 r_mcbond_other 1.939 r_angle_other_deg 1.609 r_symmetry_nbd_refined 0.314 r_symmetry_xyhbond_nbd_refined 0.266 r_xyhbond_nbd_refined 0.245 r_nbd_refined 0.244 r_nbd_other 0.213 r_nbtor_refined 0.187 r_symmetry_nbd_other 0.18 r_chiral_restr 0.119 r_symmetry_xyhbond_nbd_other 0.091 r_symmetry_nbtor_other 0.088 r_bond_refined_d 0.02 r_gen_planes_refined 0.014 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2502 Nucleic Acid Atoms Solvent Atoms 530 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing