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Crystal structure of a biodegradable plastic-degrading cutinase from Paraphoma sp. B47-9 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 0.2M Sodium acetate, 0.1M Sodium cacodylate, 1mM Calcium chloride, 30% w/v Polyethylene glycol 8000
Crystal Properties Matthews coefficient Solvent content 1.865 34.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.886 α = 103.78 b = 43.517 β = 92.42 c = 51.724 γ = 101.49
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 315 2010-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
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 1.36 36.69 89.9 0.064 0.074 0.037 0.998 16.2 3.9 55832
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 1.36 1.38 86.7 0.334 0.389 0.198 0.893 3.8
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 1.36 36.69 52937 2857 89.98 0.1242 0.122 0.1198 0.1659 0.1644 RANDOM 9.15
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] -0.23 0.6 1 0.1 0.38 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.58 r_dihedral_angle_4_deg 14.063 r_dihedral_angle_3_deg 11.498 r_rigid_bond_restr 7.271 r_dihedral_angle_1_deg 6.365 r_angle_refined_deg 2.059 r_angle_other_deg 1.673 r_chiral_restr 0.114 r_bond_refined_d 0.016 r_gen_planes_refined 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.58 r_dihedral_angle_4_deg 14.063 r_dihedral_angle_3_deg 11.498 r_rigid_bond_restr 7.271 r_dihedral_angle_1_deg 6.365 r_angle_refined_deg 2.059 r_angle_other_deg 1.673 r_chiral_restr 0.114 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2779 Nucleic Acid Atoms Solvent Atoms 360 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement Aimless data scaling SHELX phasing PDB_EXTRACT data extraction xia2 data reduction