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Inactive mutant S168A of dsPETase05 in complex with terephthalic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 4.0 M Potassium formate, 0.1 M BIS-TRIS propane 9.0, 2% w/v Polyethylene glycol monomethyl ether 2,000
Crystal Properties Matthews coefficient Solvent content 3.32 62.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.807 α = 90 b = 128.807 β = 90 c = 128.807 γ = 90
Symmetry Space Group I 21 3
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 EIGER2 X 9M 2023-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.9998 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.49 25 100 0.065 0.068 0.022 1 10.6 9.6 57879
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.49 1.54 100 0.529 0.559 0.18 0.927 9.6
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 1.49 23.53 54904 2975 99.95 0.10787 0.10653 0.1068 0.13201 0.1325 RANDOM 15.415
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 r_dihedral_angle_2_deg 34.594 r_dihedral_angle_4_deg 11.968 r_dihedral_angle_3_deg 8.81 r_dihedral_angle_1_deg 6.999 r_long_range_B_refined 6.148 r_long_range_B_other 5.331 r_rigid_bond_restr 3.029 r_scangle_other 2.976 r_scbond_it 2.694 r_scbond_other 2.693
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.594 r_dihedral_angle_4_deg 11.968 r_dihedral_angle_3_deg 8.81 r_dihedral_angle_1_deg 6.999 r_long_range_B_refined 6.148 r_long_range_B_other 5.331 r_rigid_bond_restr 3.029 r_scangle_other 2.976 r_scbond_it 2.694 r_scbond_other 2.693 r_angle_refined_deg 1.827 r_mcangle_other 1.746 r_mcangle_it 1.745 r_angle_other_deg 1.663 r_mcbond_it 1.611 r_mcbond_other 1.428 r_chiral_restr 0.102 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1889 Nucleic Acid Atoms Solvent Atoms 442 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing