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Crystal structure of S185H mutant PET hydrolase from Ideonella sakaiensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XG0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 Polyethylene Glycol 6000, Glycerol, MES
Crystal Properties Matthews coefficient Solvent content 2.04 39.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.925 α = 90 b = 51.806 β = 90 c = 84.287 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX-300 2019-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.32 25 96.7 0.045 0.049 0.018 14 7 51200
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 1.32 1.37 95.5 0.438 0.473 0.176 0.933 7
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 5XG0 1.32 24.71 48671 2481 96.65 0.1451 0.144 0.1458 0.1656 0.1672 RANDOM 13.769
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] -0.52 -0.61 1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.495 r_dihedral_angle_4_deg 15.846 r_dihedral_angle_3_deg 10.39 r_dihedral_angle_1_deg 6.828 r_angle_other_deg 1.539 r_angle_refined_deg 1.495 r_chiral_restr 0.086 r_gen_planes_refined 0.016 r_bond_refined_d 0.01 r_gen_planes_other 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.495 r_dihedral_angle_4_deg 15.846 r_dihedral_angle_3_deg 10.39 r_dihedral_angle_1_deg 6.828 r_angle_other_deg 1.539 r_angle_refined_deg 1.495 r_chiral_restr 0.086 r_gen_planes_refined 0.016 r_bond_refined_d 0.01 r_gen_planes_other 0.007 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1915 Nucleic Acid Atoms Solvent Atoms 330 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing