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Crystal structure of the deep-sea halophilic PET hydrolase dsPETase05
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 2.8 M sodium acetate trihydrate pH 7.0, 0.1 M Bis-Tris propane, pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.18 61.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.096 α = 90 b = 127.096 β = 90 c = 127.096 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 Bruker PHOTON III 2023-09-15 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 2.06 33.99 99.8 0.0811 15.51 16.24 21247
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 2.06 2.09 97.5 0.5494 2.07 6.4
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 2.06 33.99 19976 1122 99.36 0.18336 0.18101 0.1917 0.22329 0.2315 RANDOM 32.52
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 35.639 r_dihedral_angle_3_deg 13.723 r_dihedral_angle_4_deg 13.708 r_dihedral_angle_1_deg 7.679 r_long_range_B_refined 6.226 r_long_range_B_other 6.199 r_scangle_other 4.813 r_mcangle_other 3.945 r_mcangle_it 3.935 r_scbond_it 3.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.639 r_dihedral_angle_3_deg 13.723 r_dihedral_angle_4_deg 13.708 r_dihedral_angle_1_deg 7.679 r_long_range_B_refined 6.226 r_long_range_B_other 6.199 r_scangle_other 4.813 r_mcangle_other 3.945 r_mcangle_it 3.935 r_scbond_it 3.294 r_scbond_other 3.292 r_mcbond_it 2.915 r_mcbond_other 2.871 r_angle_refined_deg 1.683 r_angle_other_deg 1.459 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 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 1890 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SAINT data scaling PDB_EXTRACT data extraction SAINT data reduction PHASER phasing