5BNW

The active site of O-GlcNAc transferase imposes constraints on substrate sequence


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PE4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.42941.3 M DL-Malic acid pH 6.4, 0.1 M Bis-Tris propane pH 6.4 supplemented with crystal seeds grown out of the same condition.
Crystal Properties
Matthews coefficientSolvent content
2.2144.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138.183α = 90
b = 150.176β = 90
c = 199.241γ = 90
Symmetry
Space GroupF 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6MPilatus 2M Detector2015-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92DiamondI04-1

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
12.43099.90.10411.86.526363140463
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)
12.42.531000.7192.46.7

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 REPLACEMENTTHROUGHOUT3PE42.43038435202299.840.189810.187360.23517RANDOM45.84
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]
-1.492.89-1.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.512
r_dihedral_angle_4_deg18.421
r_dihedral_angle_3_deg15.779
r_long_range_B_other7.577
r_long_range_B_refined7.573
r_dihedral_angle_1_deg6.366
r_scangle_other5.515
r_mcangle_it4.584
r_mcangle_other4.584
r_scbond_it3.424
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.512
r_dihedral_angle_4_deg18.421
r_dihedral_angle_3_deg15.779
r_long_range_B_other7.577
r_long_range_B_refined7.573
r_dihedral_angle_1_deg6.366
r_scangle_other5.515
r_mcangle_it4.584
r_mcangle_other4.584
r_scbond_it3.424
r_scbond_other3.423
r_mcbond_it3.027
r_mcbond_other3.027
r_angle_refined_deg1.492
r_angle_other_deg0.82
r_chiral_restr0.081
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms5533
Nucleic Acid Atoms
Solvent Atoms78
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
Cootmodel building
MOLREPphasing