5FOE

Crystal structure of the C. elegans Protein O-fucosyltransferase 2 (CePOFUT2) double mutant (R298K-R299K) in complex with GDP and the human TSR1 from thrombospondin 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4AP5PDB ENTRY 4AP5

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.1542.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.026α = 90
b = 67.447β = 116.07
c = 90.411γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
11.982099.80.18.24.32836362
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.982.0999.90.6924.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4AP51.9881.2164467185299.790.201680.200440.24607RANDOM35.795
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]
-0.510.420.030.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.372
r_dihedral_angle_3_deg16.347
r_dihedral_angle_4_deg15.853
r_dihedral_angle_1_deg6.728
r_mcangle_it2.369
r_scbond_it1.662
r_angle_refined_deg1.565
r_mcbond_it1.464
r_mcbond_other1.464
r_angle_other_deg1.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.372
r_dihedral_angle_3_deg16.347
r_dihedral_angle_4_deg15.853
r_dihedral_angle_1_deg6.728
r_mcangle_it2.369
r_scbond_it1.662
r_angle_refined_deg1.565
r_mcbond_it1.464
r_mcbond_other1.464
r_angle_other_deg1.079
r_chiral_restr0.089
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.004
r_gen_planes_other0.004
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7150
Nucleic Acid Atoms
Solvent Atoms531
Heterogen Atoms124

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing