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Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S mutant in Zn(2+)-bound state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WFJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.01 M ZnSO4, 0.1 M MES pH 6.5, 25% v/v PEG MME 550
Crystal Properties Matthews coefficient Solvent content 2.15 42.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.196 α = 90 b = 63.243 β = 90 c = 78.675 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 MX225HE 2016-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.8000 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.12 50 95.3 0.057 0.999 18.9 6.5 93489 7.55585109261
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.12 1.18 75.1 0.282 0.908 4.1 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 4WFJ 1.12 42.3167097133 1.35011784998 93488 4688 95.3239390664 0.121787925587 0.120723929286 0.1209 0.141836601104 0.1414 Random selection 11.1557748294
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 12.0570903882 f_angle_d 1.27950165828 f_chiral_restr 0.0846484310707 f_plane_restr 0.00836946675578 f_bond_d 0.00703871777744
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2042 Nucleic Acid Atoms Solvent Atoms 441 Heterogen Atoms 29
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing