5UN9

The crystal structure of human O-GlcNAcase in complex with Thiamet-G


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5TKE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION2930.128 M potassium thiocyanate, 0.032 M ammonium citrate tribasic (pH 7.0), 0.016 M imidazole (pH 7.0), 0.002 M zinc sulfate heptahydrate, 0.02 M MES monohydrate (pH 6.5), 12.8% w/v polyethylene glycol 3,350, 3.2% w/v polyethylene glycol monomethyl ether 2,000, 5% v/v polyethylene glycol monomethyl ether 550
Crystal Properties
Matthews coefficientSolvent content
2.9358

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.572α = 90
b = 96.106β = 115.01
c = 89.534γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDMARMOSAIC 225 mm CCD2016-06-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.978APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.53099.50.063235.344310
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)
12.52.5495.10.2780.78525.2

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-VALUE5TKE2.529.7971.3542091210794.650.21270.21030.2604Random
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_d18.808
f_angle_d1.211
f_chiral_restr0.065
f_bond_d0.011
f_plane_restr0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6922
Nucleic Acid Atoms
Solvent Atoms238
Heterogen Atoms32

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing