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Crystal structure of PETase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224E/N233C/S242T/N246D/N275C/S282C/F284C mutant from Ideonella sakaiensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ILW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 285 20 % PEG3350 and 0.2 M potassium iodide
Crystal Properties Matthews coefficient Solvent content 2.38 48.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.168 α = 90 b = 51.546 β = 119.09 c = 100.37 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 270 2021-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
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 1.7 50 95.8 0.971 7.3 2.8 185509
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 1.7 1.73 90.5 0.649 2.7
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 5XJH 1.7 27.97 91891 4474 96.83 0.15595 0.15458 0.1743 0.18475 0.2013 RANDOM 13.236
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] 0.27 0.46 -0.94 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.711 r_dihedral_angle_2_deg 8.979 r_dihedral_angle_1_deg 6.902 r_long_range_B_refined 5.613 r_long_range_B_other 4.719 r_scangle_other 2.897 r_scbond_it 2.001 r_scbond_other 2.001 r_mcangle_it 1.929 r_mcangle_other 1.929
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.711 r_dihedral_angle_2_deg 8.979 r_dihedral_angle_1_deg 6.902 r_long_range_B_refined 5.613 r_long_range_B_other 4.719 r_scangle_other 2.897 r_scbond_it 2.001 r_scbond_other 2.001 r_mcangle_it 1.929 r_mcangle_other 1.929 r_angle_refined_deg 1.646 r_mcbond_it 1.319 r_mcbond_other 1.315 r_angle_other_deg 0.578 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 5762 Nucleic Acid Atoms Solvent Atoms 1038 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction PDB_EXTRACT data extraction HKL-2000 data scaling MOLREP phasing