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Crystal structure of an engineered PETase, EV2, derived from Thermobifida fusca cutinase (TfCut2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LUK made a model from 5luk
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 290 0.2M Sodium acetate, 0.1 M MES (4.6), 20% PEG 8K
Crystal Properties Matthews coefficient Solvent content 2.15 42.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.37 α = 97.96 b = 42.38 β = 91.6 c = 69.18 γ = 101.94
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 EIGER X 16M Rh coated collimating mirrors, K-B focusing mirrors 2024-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.08 37.71 89.2 0.081 0.089 0.998 10.94 5.3 178134
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.08 1.11 0.692 0.815 0.814
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.08 37.71 1.97 178115 8907 89.14 0.1372 0.1361 0.1362 0.1589 0.1591
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.325 f_angle_d 1.266 f_chiral_restr 0.108 f_plane_restr 0.016 f_bond_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3935 Nucleic Acid Atoms Solvent Atoms 675 Heterogen Atoms 13
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling XDS data reduction MOLREP phasing