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Crystal structure of PETase S121E, D186H 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 6.5 293 Tris, PEG 3000, NaCl
Crystal Properties Matthews coefficient Solvent content 1.94 36.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.198 α = 90 b = 50.864 β = 92.7 c = 41.486 γ = 90
Symmetry Space Group C 1 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 2018-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim 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 1.85 50 98.3 0.068 25.56 3.3 19977
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 0.223
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5xjh 1.86 31.28 18959 1018 97.01 0.20688 0.20467 0.2157 0.24685 0.2561 RANDOM 28.597
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] 0.41 -3.68 -1.64 1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.796 r_dihedral_angle_4_deg 19.33 r_dihedral_angle_3_deg 14.046 r_dihedral_angle_1_deg 7.593 r_long_range_B_refined 5.422 r_long_range_B_other 5.42 r_scangle_other 3.77 r_mcangle_it 2.97 r_mcangle_other 2.97 r_scbond_it 2.548
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.796 r_dihedral_angle_4_deg 19.33 r_dihedral_angle_3_deg 14.046 r_dihedral_angle_1_deg 7.593 r_long_range_B_refined 5.422 r_long_range_B_other 5.42 r_scangle_other 3.77 r_mcangle_it 2.97 r_mcangle_other 2.97 r_scbond_it 2.548 r_scbond_other 2.546 r_mcbond_it 2.081 r_mcbond_other 2.08 r_angle_refined_deg 1.592 r_angle_other_deg 1.335 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 1927 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling HKL-2000 data collection Coot model building MOLREP phasing