5NPR

The human O-GlcNAc transferase in complex with a thiol-linked bisubstrate inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.4295Reservoir solution: 1.45 M K2HPO4, 8 mM EDTA, 1% xylitol Drop solution: 1.45 M K2HPO4, 8 mM EDTA, 1% xylitol, 0.5 M (NH4)2SO4, crystal seeds Seeds were generated from crystals grown in 1.3 M DL-Malic acid, 0.1 M Bis-Tris propane pH 6.4
Crystal Properties
Matthews coefficientSolvent content
3.3363

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138.038α = 90
b = 150.951β = 90
c = 200.54γ = 90
Symmetry
Space GroupF 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.976ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rpim 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
11.8546.0199.50.060.0780.0480.999.7488158
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.8899.80.8711.2020.7110.651.34.1

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 REPLACEMENTTHROUGHOUT3PE41.8546.0183781436999.420.20650.204970.23641RANDOM46.58
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]
-2.794.54-1.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.605
r_dihedral_angle_4_deg18.311
r_dihedral_angle_3_deg13.492
r_long_range_B_refined6.534
r_long_range_B_other6.466
r_dihedral_angle_1_deg6.026
r_scangle_other4.74
r_mcangle_other3.723
r_mcangle_it3.721
r_scbond_it2.912
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.605
r_dihedral_angle_4_deg18.311
r_dihedral_angle_3_deg13.492
r_long_range_B_refined6.534
r_long_range_B_other6.466
r_dihedral_angle_1_deg6.026
r_scangle_other4.74
r_mcangle_other3.723
r_mcangle_it3.721
r_scbond_it2.912
r_scbond_other2.912
r_mcbond_it2.499
r_mcbond_other2.498
r_angle_refined_deg1.408
r_angle_other_deg0.968
r_chiral_restr0.082
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5564
Nucleic Acid Atoms
Solvent Atoms362
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building