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X-ray structure of SCoV2-PLpro in complex with small molecule inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6W9C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.05 M Sodium cacodylate pH 6.5
0.2 M Potassium chloride,
0.1 M Magnesium acetate
10 %(w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.45 64.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.37 α = 90 b = 116.37 β = 90 c = 253.566 γ = 120
Symmetry Space Group P 65 2 2
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 2M-F 2020-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000 SLS X06DA
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 2.678 49.47 95.7 0.99 13.2 38.1 21442
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 2.678 2.969 0.699 1.8
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 (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 6W9C 2.68 49.47 20369 1001 72.64 0.1965 0.1932 0.1937 0.2641 0.2636 RANDOM 42.655
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] -0.76 -0.38 -0.76 2.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.76 r_dihedral_angle_3_deg 21.707 r_dihedral_angle_4_deg 18.846 r_dihedral_angle_1_deg 8.171 r_angle_refined_deg 2.011 r_chiral_restr 0.148 r_bond_refined_d 0.013 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4805 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 151
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction STARANISO data scaling PHASER phasing