7CW1

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).


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.17M Sodium acetate trihydrate, 0.085M Sodium cacodylate trihydrate , 25.5%w/v Polyethylene glycol 8000, 15%w/v Polyethylene glycol 400
Crystal Properties
Matthews coefficientSolvent content
1.83933.157

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.065α = 90
b = 61.587β = 90
c = 110.387γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2017-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0Photon FactoryBL-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.755.1998.30.1170.1220.0340.9981712.933315
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)RedundancyNumber Unique Reflections (All)
11.71.73960.4870.5070.1390.93312.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.755.1931548171398.090.15760.15580.1911RANDOM9.31
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]
-0.14-0.270.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.162
r_dihedral_angle_4_deg19.603
r_dihedral_angle_3_deg11.061
r_dihedral_angle_1_deg6.673
r_angle_refined_deg1.684
r_angle_other_deg1.594
r_chiral_restr0.096
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.162
r_dihedral_angle_4_deg19.603
r_dihedral_angle_3_deg11.061
r_dihedral_angle_1_deg6.673
r_angle_refined_deg1.684
r_angle_other_deg1.594
r_chiral_restr0.096
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2846
Nucleic Acid Atoms
Solvent Atoms361
Heterogen Atoms11

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
CRANK2phasing