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The crystal structure of wild-type Papain-Like Protease of SARS-CoV-2 with TDI-016675-CL-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 5.6 291 0.2 M Ammonium sulfate, 0.1 M tri-Sodium citrate (pH 5.6) and 15% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.02 59.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.63 α = 90 b = 97.39 β = 90 c = 146.49 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 X 9M 2023-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1.00003 NSRRC TPS 05A
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 1.89 48.83 99.7 0.123 0.136 0.058 0.999 11.5 9.9 70080
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 1.89 1.93 99.5 1.229 1.372 0.6 0.88 2.2 9.5
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-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 1.89 48.742 69994 3465 99.667 0.222 0.22172 0.2213 0.2356 0.2305 0.2434 RANDOM 30.251
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] -3.059 4.966 -1.907
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.002 r_dihedral_angle_3_deg 13.718 r_dihedral_angle_1_deg 5.997 r_lrange_it 4.954 r_lrange_other 4.654 r_scangle_it 2.664 r_scangle_other 2.663 r_mcangle_other 2.223 r_mcangle_it 2.222 r_scbond_it 1.577
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.002 r_dihedral_angle_3_deg 13.718 r_dihedral_angle_1_deg 5.997 r_lrange_it 4.954 r_lrange_other 4.654 r_scangle_it 2.664 r_scangle_other 2.663 r_mcangle_other 2.223 r_mcangle_it 2.222 r_scbond_it 1.577 r_scbond_other 1.577 r_mcbond_it 1.372 r_mcbond_other 1.371 r_angle_refined_deg 1.358 r_angle_other_deg 0.893 r_dihedral_angle_2_deg 0.55 r_nbd_other 0.237 r_nbd_refined 0.194 r_symmetry_nbd_other 0.194 r_symmetry_xyhbond_nbd_refined 0.189 r_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.159 r_symmetry_nbd_refined 0.127 r_metal_ion_refined 0.103 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.058 r_bond_refined_d 0.014 r_gen_planes_other 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5016 Nucleic Acid Atoms Solvent Atoms 703 Heterogen Atoms 186
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PHASER phasing Coot model building