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Crystal structure 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 0.1 M Bis-Tris propane pH 7.0, 3 M sodium
acetate
Crystal Properties Matthews coefficient Solvent content 3.29 62.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.473 α = 90 b = 128.473 β = 90 c = 128.473 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 2023-09-30 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 1.5 25 100 0.083 0.088 0.03 0.996 9.7 9.3 56330
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 1.5 1.55 100 0.817 0.865 0.282 0.855 9.4
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 1.5 23.47 53364 2966 99.93 0.10261 0.10075 0.1013 0.13704 0.1371 RANDOM 18.617
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 34.462 r_dihedral_angle_3_deg 10.614 r_dihedral_angle_4_deg 8.887 r_dihedral_angle_1_deg 6.805 r_long_range_B_refined 4.914 r_rigid_bond_restr 4.583 r_scangle_other 4.517 r_long_range_B_other 4.206 r_scbond_other 3.653 r_scbond_it 3.649
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.462 r_dihedral_angle_3_deg 10.614 r_dihedral_angle_4_deg 8.887 r_dihedral_angle_1_deg 6.805 r_long_range_B_refined 4.914 r_rigid_bond_restr 4.583 r_scangle_other 4.517 r_long_range_B_other 4.206 r_scbond_other 3.653 r_scbond_it 3.649 r_mcangle_other 2.667 r_mcangle_it 2.654 r_mcbond_it 2.362 r_mcbond_other 2.327 r_angle_refined_deg 1.89 r_angle_other_deg 1.673 r_chiral_restr 0.113 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1890 Nucleic Acid Atoms Solvent Atoms 331 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing