6Q4M

Crystal structure of the O-GlcNAc transferase Asn648Tyr mutation

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	1.45 M K2HPO4, 8 mM EDTA and 1% xylitol.

Crystal Properties
Matthews coefficient	Solvent content
3.19	61.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.316	α = 90
b = 150.736	β = 90
c = 199.492	γ = 90

Symmetry
Space Group	F 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2017-12-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.873	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.2	45.92	99.9	12	6.7		52373

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.27

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.2	45.92	49733	2638	99.98	0.17589	0.17464	0.19886	RANDOM	50.781

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]
-0.17			3.53		-3.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.661
r_dihedral_angle_4_deg	21.453
r_dihedral_angle_3_deg	15.941
r_long_range_B_refined	11.238
r_long_range_B_other	11.177
r_scangle_other	8.872
r_mcangle_it	7.001
r_mcangle_other	7.001
r_dihedral_angle_1_deg	6.765
r_scbond_it	6.187
r_scbond_other	6.018
r_mcbond_it	4.971
r_mcbond_other	4.967
r_angle_refined_deg	1.79
r_angle_other_deg	1.435
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	5519
Nucleic Acid Atoms
Solvent Atoms	370
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing