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Crystal strcuture of PETase A248D, R280K mutant from Ideonella sakaiensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XJH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 17% PEG 10K, 0.1M Bis-Tris, pH 5.0, 0.15M Ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.15 42.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.236 α = 90 b = 51.236 β = 90 c = 179.091 γ = 120
Symmetry Space Group P 31 2 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 CCD ADSC QUANTUM 270 2019-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97834 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.9 50 98.1 0.148 55.22 9.6 21740
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 0.332
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5xjh 1.91 27.89 20619 1078 97.88 0.1574 0.1557 0.1911 0.2117 RANDOM 9.899
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 -0.16 -0.33 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.892 r_dihedral_angle_4_deg 19.064 r_dihedral_angle_3_deg 12.413 r_dihedral_angle_1_deg 6.928 r_angle_refined_deg 1.752 r_angle_other_deg 1.533 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.892 r_dihedral_angle_4_deg 19.064 r_dihedral_angle_3_deg 12.413 r_dihedral_angle_1_deg 6.928 r_angle_refined_deg 1.752 r_angle_other_deg 1.533 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1940 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data reduction REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data scaling MOLREP phasing