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Crystal structure of a biodegradable plastic-degrading cutinase-like enzyme from the phyllosphere yeast, Pseudozyma antarctica, solved by getting the phase from anomalous scattering of uncovalently coordinated arsenic (cacodylate).
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.17M Sodium acetate trihydrate, 0.085M Sodium cacodylate trihydrate , 25.5%w/v Polyethylene glycol 8000, 15%w/v Polyethylene glycol 400
Crystal Properties Matthews coefficient Solvent content 1.839 33.157
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.065 α = 90 b = 61.587 β = 90 c = 110.387 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 PIXEL DECTRIS PILATUS3 S 6M 2017-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 1.7 55.19 98.3 0.117 0.122 0.034 0.998 17 12.9 33315
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 1.7 1.73 96 0.487 0.507 0.139 0.933 12.9
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.7 55.19 31548 1713 98.09 0.1576 0.1558 0.1702 0.1911 0.2011 RANDOM 9.31
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] -0.14 -0.27 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.162 r_dihedral_angle_4_deg 19.603 r_dihedral_angle_3_deg 11.061 r_dihedral_angle_1_deg 6.673 r_angle_refined_deg 1.684 r_angle_other_deg 1.594 r_chiral_restr 0.096 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.162 r_dihedral_angle_4_deg 19.603 r_dihedral_angle_3_deg 11.061 r_dihedral_angle_1_deg 6.673 r_angle_refined_deg 1.684 r_angle_other_deg 1.594 r_chiral_restr 0.096 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2846 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms 11
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction CRANK2 phasing