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Crystal structure of the deep-sea halophilic PET hydrolase dsPETase01
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 Sodium Fluoride,25% w/v
Polyethylene Glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.11 41.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.279 α = 90 b = 44.916 β = 92.82 c = 73.16 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 PIXEL DECTRIS EIGER2 X 16M 2024-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 07A 0.9762 NSRRC TPS 07A
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 1.61 25 96.3 0.059 0.07 0.036 0.991 11.2 3.5 57132
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 1.61 1.67 81.5 0.302 0.379 0.224 0.839 2.5
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 1.61 24.72 54329 2790 96.12 0.1588 0.15683 0.1691 0.19675 0.2021 RANDOM 20.312
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] 0.8 -0.36 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.841 r_dihedral_angle_4_deg 21.014 r_dihedral_angle_3_deg 12.168 r_dihedral_angle_1_deg 6.796 r_long_range_B_refined 4.504 r_long_range_B_other 4.252 r_scangle_other 3.346 r_scbond_it 2.323 r_scbond_other 2.322 r_mcangle_it 1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.841 r_dihedral_angle_4_deg 21.014 r_dihedral_angle_3_deg 12.168 r_dihedral_angle_1_deg 6.796 r_long_range_B_refined 4.504 r_long_range_B_other 4.252 r_scangle_other 3.346 r_scbond_it 2.323 r_scbond_other 2.322 r_mcangle_it 1.98 r_mcangle_other 1.98 r_angle_refined_deg 1.752 r_angle_other_deg 1.522 r_mcbond_it 1.518 r_mcbond_other 1.514 r_chiral_restr 0.093 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 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 3864 Nucleic Acid Atoms Solvent Atoms 580 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing