7CY9

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).


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.2M Sodium acetate, 0.1M Sodium cacodylate, 1mM Calcium chloride, 30% w/v Polyethylene glycol 8000
Crystal Properties
Matthews coefficientSolvent content
1.86534.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.886α = 103.78
b = 43.517β = 92.42
c = 51.724γ = 101.49
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-11-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.0SPring-8BL38B1

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
11.3636.6989.90.0640.0740.0370.99816.23.955832
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)
11.361.3886.70.3340.3890.1980.8933.8

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 DIFFRACTIONSADTHROUGHOUT1.3636.6952937285789.980.12420.1220.1659RANDOM9.15
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]
-0.230.610.10.38-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.58
r_dihedral_angle_4_deg14.063
r_dihedral_angle_3_deg11.498
r_rigid_bond_restr7.271
r_dihedral_angle_1_deg6.365
r_angle_refined_deg2.059
r_angle_other_deg1.673
r_chiral_restr0.114
r_bond_refined_d0.016
r_gen_planes_refined0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.58
r_dihedral_angle_4_deg14.063
r_dihedral_angle_3_deg11.498
r_rigid_bond_restr7.271
r_dihedral_angle_1_deg6.365
r_angle_refined_deg2.059
r_angle_other_deg1.673
r_chiral_restr0.114
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2779
Nucleic Acid Atoms
Solvent Atoms360
Heterogen Atoms19

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
SHELXphasing
PDB_EXTRACTdata extraction
xia2data reduction