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Crystal structure of BHEF-bound PETase (S160A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9M8H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 0.1M sodium citrate (pH5.0), 0.2M sodium citrate, 24% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.7 66.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.402 α = 90 b = 76.402 β = 90 c = 119.987 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 PILATUS 6M 2024-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.0 SPring-8 BL45XU
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 2.49 44.44 99.5 0.127 0.151 0.09 0.99 9.21 5.14 27162 29.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.49 2.65 97.2 0.284 0.241 0.975 5.1
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.49 44.44 27128 1356 98.62 0.1959 0.1934 0.1934 0.244 0.2437 33.98
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 f_dihedral_angle_d 12.5476 f_angle_d 0.5419 f_chiral_restr 0.0452 f_plane_restr 0.0052 f_bond_d 0.0033
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3859 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 34
Software Software Software Name Purpose PHENIX refinement XDS data scaling Coot model building PHASER phasing XDS data reduction