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SARS-CoV-2 papain-like-protease (PLpro) in complex with inhibitor Linagliptin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WZU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 0.1 M Tris-HCl (pH 7.5-9.0), 1.4 M NaH2PO4, 2-15% Glycerol
Crystal Properties Matthews coefficient Solvent content 3.54 65.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.217 α = 90 b = 81.217 β = 90 c = 133.485 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 RIGAKU HyPix-6000HE 2023-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.7 23.09 99.8 0.06 10.7 4 16226
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.83 100 0.41 2
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.7 23 14471 684 99.717 0.224 0.2208 0.2207 0.2882 0.2882 45.378
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] 0.553 0.276 0.553 -1.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.644 r_lrange_it 14.067 r_dihedral_angle_6_deg 13.451 r_scangle_it 8.473 r_dihedral_angle_2_deg 7.581 r_dihedral_angle_1_deg 7.376 r_mcangle_it 6.566 r_scbond_it 5.511 r_mcbond_it 4.11 r_angle_refined_deg 1.968
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.644 r_lrange_it 14.067 r_dihedral_angle_6_deg 13.451 r_scangle_it 8.473 r_dihedral_angle_2_deg 7.581 r_dihedral_angle_1_deg 7.376 r_mcangle_it 6.566 r_scbond_it 5.511 r_mcbond_it 4.11 r_angle_refined_deg 1.968 r_nbtor_refined 0.319 r_nbd_refined 0.257 r_symmetry_nbd_refined 0.255 r_symmetry_xyhbond_nbd_refined 0.245 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.138 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2502 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing