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SARS-CoV-2 Papain like protease (PLpro) in complex with inhibitor Lithocholic acid
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 3.590202 65.76138
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.732 α = 90 b = 81.732 β = 90 c = 133.689 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 2023-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.3 24.84 99.9 0.172 0.913 2.5 4 23592
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 99.9 0.576 0.381 0.616 5.4
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.3 24.838 23561 1207 99.86 0.241 0.2386 0.2259 0.2844 0.2656 37.53
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] -0.49 -0.49 0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.578 r_dihedral_angle_6_deg 12.957 r_lrange_it 10.275 r_dihedral_angle_1_deg 8.772 r_dihedral_angle_2_deg 8.294 r_scangle_it 6.185 r_mcangle_it 5.906 r_scbond_it 4.518 r_mcbond_it 4.242 r_angle_refined_deg 2.535
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.578 r_dihedral_angle_6_deg 12.957 r_lrange_it 10.275 r_dihedral_angle_1_deg 8.772 r_dihedral_angle_2_deg 8.294 r_scangle_it 6.185 r_mcangle_it 5.906 r_scbond_it 4.518 r_mcbond_it 4.242 r_angle_refined_deg 2.535 r_symmetry_nbd_refined 0.418 r_nbtor_refined 0.334 r_nbd_refined 0.276 r_symmetry_xyhbond_nbd_refined 0.257 r_xyhbond_nbd_refined 0.241 r_chiral_restr 0.208 r_gen_planes_refined 0.009 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2501 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing