5ZRQ

Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S mutant in Zn(2+)-bound state


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4WFJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.01 M ZnSO4, 0.1 M MES pH 6.5, 25% v/v PEG MME 550
Crystal Properties
Matthews coefficientSolvent content
2.1542.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.196α = 90
b = 63.243β = 90
c = 78.675γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2016-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B10.8000SPring-8BL38B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
11.125095.30.0570.99918.96.5934897.55585109261
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)RedundancyNumber Unique Reflections (All)
11.121.1875.10.2820.9084.13.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4WFJ1.1242.31670971331.3501178499893488468895.32393906640.1217879255870.1207239292860.141836601104Random selection11.1557748294
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.0570903882
f_angle_d1.27950165828
f_chiral_restr0.0846484310707
f_plane_restr0.00836946675578
f_bond_d0.00703871777744
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2042
Nucleic Acid Atoms
Solvent Atoms441
Heterogen Atoms29

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing