6IBO

Catalytic deficiency of O-GlcNAc transferase leads to X-linked intellectual disability

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5C1D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	1.45 M K2HPO4, 8 mM EDTA and 1% xylitol

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.737	α = 90
b = 150.617	β = 90
c = 199.996	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	80	PIXEL	DECTRIS PILATUS 6M		2018-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.99187	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	1.5	100	100	11.3	5.2		286887

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.17	2.23	99		0.91	0.848	1.3	5.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	5C1D	2.17	100	51399	2677	98.66	0.2035	0.20086	0.25368	RANDOM	54.861

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]
-1.93			4.7		-2.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.025
r_dihedral_angle_4_deg	20.378
r_dihedral_angle_3_deg	15.798
r_long_range_B_refined	9.782
r_long_range_B_other	9.763
r_scangle_other	7.685
r_dihedral_angle_1_deg	6.939
r_mcangle_it	6.76
r_mcangle_other	6.76
r_scbond_it	5.296
r_scbond_other	5.169
r_mcbond_it	4.955
r_mcbond_other	4.954
r_angle_refined_deg	1.781
r_angle_other_deg	1.06
r_chiral_restr	0.098
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002
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 Atoms	Number
Protein Atoms	5528
Nucleic Acid Atoms
Solvent Atoms	318
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing