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Crystal structure of Pichia pastoris-expressed FAST-PETase-N212A/K233C/S282C variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8J45
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 298 25% PEG 1500, 0.1 M MMT, pH 9.0
Crystal Properties Matthews coefficient Solvent content 1.99 38.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51 α = 90 b = 51.018 β = 90 c = 83.971 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 Bruker PHOTON III 2023-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE BRUKER METALJET 1.34138
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.71 33.16 99.5 0.0337 40.32 8.76 24277
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.71 1.81 99.1 0.0674 3.89
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 (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 1.71 33.16 22997 1190 99.37 0.13977 0.13816 0.1518 0.17129 0.1839 RANDOM 11.81
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] 0.13 0.12 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.015 r_dihedral_angle_4_deg 15.994 r_dihedral_angle_3_deg 11.877 r_dihedral_angle_1_deg 7.042 r_long_range_B_refined 3.993 r_long_range_B_other 3.8 r_scangle_other 2.85 r_angle_refined_deg 1.95 r_scbond_it 1.896 r_scbond_other 1.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.015 r_dihedral_angle_4_deg 15.994 r_dihedral_angle_3_deg 11.877 r_dihedral_angle_1_deg 7.042 r_long_range_B_refined 3.993 r_long_range_B_other 3.8 r_scangle_other 2.85 r_angle_refined_deg 1.95 r_scbond_it 1.896 r_scbond_other 1.896 r_angle_other_deg 1.657 r_mcangle_it 1.539 r_mcangle_other 1.538 r_mcbond_it 1.027 r_mcbond_other 1.027 r_chiral_restr 0.103 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1922 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement SAINT data scaling SAINT data reduction PHASER phasing