6GRW

Glucuronoyl Esterase from Opitutus terrae (Au derivative)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherStructure under deposition

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8293.15Reservoir composition for crystal growth: 0.03M Magnesium chloride, 0.03 M calcium chloride, 0.05M imidazole, 0.05M MES, 10% v/v MPD, 10% w/v PEG 1000, 10% v/w PEG 3500P. Heavy atom derivatization: 1.2uL crystallization mother liquor containing 0.5mM KAu(CN)2 added to drop containing crystals. Drop size and composition: Sitting drops of 0.4ul were mixed in a protein:reservoir volume ratio of 1:1 using 45 mg/mL of OtCE15A in 20 mM TRIS pH 8.0
Crystal Properties
Matthews coefficientSolvent content
1.9637.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.693α = 76.573
b = 44.608β = 67.172
c = 50.558γ = 70.648
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-08-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P110.979PETRA III, DESYP11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.546.2795.90.0420.050.99916.693.555080214.57
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5993.30.3140.370.9233.43.6

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-VALUEStructure under deposition1.546.271.9950799210196.10.13550.13450.158520.16
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_d17.5942
f_angle_d1.0928
f_chiral_restr0.0764
f_plane_restr0.0092
f_bond_d0.0083
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3073
Nucleic Acid Atoms
Solvent Atoms402
Heterogen Atoms33

Software

Software
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
PHENIXphasing
XSCALEdata scaling