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The crystal structure of wild-type Papain-Like Protease of SARS-CoV-2 with TDI-016399-NX-1
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 6.6 291 0.2 M di-Ammonium tartrate (pH 6.6) and 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.82 56.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.92 α = 90 b = 145.15 β = 99.768 c = 60.14 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 PILATUS3 6M 2023-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.00000 SPring-8 BL45XU
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 2.11 48.38 98.6 0.071 0.086 0.048 0.998 15.4 5.9 44654
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 2.11 2.17 86.4 0.206 0.262 0.16 0.952 4.9 4.4
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.113 45.948 44621 2240 98.538 0.15 0.1474 0.1579 0.1968 0.201 RANDOM 21.275
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] 0.081 -0.214 0.756 -0.721
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.757 r_dihedral_angle_6_deg 16.277 r_dihedral_angle_3_deg 13.819 r_dihedral_angle_1_deg 6.34 r_lrange_it 6.277 r_lrange_other 6.226 r_scangle_it 4.325 r_scangle_other 4.325 r_mcangle_it 2.981 r_mcangle_other 2.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.757 r_dihedral_angle_6_deg 16.277 r_dihedral_angle_3_deg 13.819 r_dihedral_angle_1_deg 6.34 r_lrange_it 6.277 r_lrange_other 6.226 r_scangle_it 4.325 r_scangle_other 4.325 r_mcangle_it 2.981 r_mcangle_other 2.981 r_scbond_it 2.777 r_scbond_other 2.776 r_mcbond_it 1.961 r_mcbond_other 1.961 r_angle_refined_deg 1.452 r_angle_other_deg 0.491 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.209 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.18 r_nbd_other 0.175 r_metal_ion_refined 0.158 r_symmetry_nbd_refined 0.157 r_symmetry_xyhbond_nbd_refined 0.15 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5016 Nucleic Acid Atoms Solvent Atoms 699 Heterogen Atoms 158
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building