7B7H

The glucuronoyl esterase OtCE15A R268A variant from Opitutus terrae in complex with, and covalently linked to, D-glucuronate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5298Morpheus screen consisting of 0.1 M buffer system 1 (imidazole and MES), 30% precipitant mix 2 (ethylene glycol and PEG 8000) and amino acid additives (L-Glutamate, Alanine (racemic); Glycine; Lysine HCl (racemic); Serine (racemic)). Soaking was carried out in a saturated solution of Bnz-GlcA in 10% DMSO and 90% mother liquor for 30 seconds before being flash frozen.
Crystal Properties
Matthews coefficientSolvent content
238.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.333α = 61.947
b = 47.298β = 67.92
c = 51.112γ = 88.272
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX1.008MAX IVBioMAX

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.79643.1596.620.12020.9956.843.63217125.74
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.7961.86192.991.2560.4610.953.6

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-VALUE6GS01.843.151.9732152198896.620.18510.18260.222432.54
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_d14.3775
f_angle_d0.897
f_chiral_restr0.054
f_plane_restr0.008
f_bond_d0.0069
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2868
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms126

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling