5UB5

human POGLUT1 in complex with human Notch1 EGF12 S458T mutant and UDP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5L0R 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529520% (v/v) PEG5000 MME, 50 mM MES pH 6.5, 2mM CaCl2, 250mM NaCl, 5% (v/v) 2-methyl-2,4-pentanediol
Crystal Properties
Matthews coefficientSolvent content
2.3647.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.951α = 90
b = 74.072β = 90
c = 83.583γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBRUKER PHOTON 1002016-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER TURBO X-RAY SOURCE1.5418

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
12.08920.998.960.090680.99818.74112648621.44
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)
12.0892.16491.490.54860.8263.165.3

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-VALUE5L0R2.08920.8961.35264791365990.15470.15260.1931032.9548
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_d12.287
f_angle_d1.235
f_chiral_restr0.071
f_bond_d0.012
f_plane_restr0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3246
Nucleic Acid Atoms
Solvent Atoms337
Heterogen Atoms121

Software

Software
Software NamePurpose
PHENIXrefinement
SAINTdata scaling
PDB_EXTRACTdata extraction
SAINTdata reduction
PHASERphasing