6T0E

The glucuronoyl esterase OtCE15A S267A variant from Opitutus terrae in complex with benzyl D-glucuronoate and D-glucuronate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6GS0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5298Enzyme mixed 50/50 with reservoir solution containing JCSG+ screen solution G4: 0.2 M Trimethylamine N-oxide, 0.1 M Tris pH 8.5, and 20 % w/v PEG 2000 MME
Crystal Properties
Matthews coefficientSolvent content
2.1442.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.719α = 90
b = 87.611β = 90
c = 173.91γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2018-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-30.9677ESRFMASSIF-3

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
11.8944.4598.980.15890.16510.044360.99912.2513.66351433.05
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.891.96920.62060.4030.8413.4

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6gs01.8944.451.3363362198898.630.16380.16220.215539.74
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_d22.8048
f_angle_d1.121
f_chiral_restr0.0623
f_bond_d0.0105
f_plane_restr0.0079
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6081
Nucleic Acid Atoms
Solvent Atoms412
Heterogen Atoms344

Software

Software
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHENIXphasing
PHENIXrefinement