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Crystal structure of the deep-sea halophilic PET hydrolase dsPETase06 C23A mutant
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 0.2M Magnesium chloride hexahydrate; 0.1M Sodium HEPES pH 7.5; 30% PEG 400
Crystal Properties Matthews coefficient Solvent content 3.39 63.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.315 α = 90 b = 77.315 β = 90 c = 116.3 γ = 120
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 2024-07-19 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 1.38 25 98.3 0.058 0.063 0.025 0.996 11 5.9 79329
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 1.38 1.43 95.4 0.626 0.682 0.267 0.873 6.1
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 1.38 24.74 75309 3970 98.29 0.13241 0.13145 0.1316 0.15102 0.1513 RANDOM 19.271
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] 0.33 0.17 0.33 -1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.576 r_dihedral_angle_4_deg 23.081 r_dihedral_angle_3_deg 10.498 r_dihedral_angle_1_deg 6.449 r_long_range_B_refined 5.527 r_long_range_B_other 5.178 r_scangle_other 4.335 r_scbond_other 2.936 r_scbond_it 2.935 r_mcangle_other 2.214
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.576 r_dihedral_angle_4_deg 23.081 r_dihedral_angle_3_deg 10.498 r_dihedral_angle_1_deg 6.449 r_long_range_B_refined 5.527 r_long_range_B_other 5.178 r_scangle_other 4.335 r_scbond_other 2.936 r_scbond_it 2.935 r_mcangle_other 2.214 r_mcangle_it 2.206 r_angle_refined_deg 2.08 r_angle_other_deg 1.657 r_mcbond_it 1.422 r_mcbond_other 1.396 r_chiral_restr 0.126 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 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 1995 Nucleic Acid Atoms Solvent Atoms 393 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing