6TKA

Crystal structure of human O-GlcNAc transferase bound to substrate 7 and a peptide from HCF-1 pro-repeat 2 (11-26)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4N39

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	1.45 M Potassium Sodium Tartrate 0.1 M Tris pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.859	α = 90
b = 100.859	β = 90
c = 132.629	γ = 120

Symmetry
Space Group	P 32 2 1

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 PILATUS 6M-F		2019-05-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9159	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.91	87.32	100	0.1	0.104	0.03	1	15.6	12		61015

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.91	1.96	100		0.71	0.405	1.1	12.3

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4n39	1.91	72.95	60965	3089	99.962	0.187	0.1845	0.2332	Random Selection	38.52

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]
0.162	0.081		0.162		-0.527

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.853
r_dihedral_angle_3_deg	16.081
r_dihedral_angle_4_deg	15.915
r_lrange_it	6.355
r_lrange_other	6.355
r_dihedral_angle_1_deg	6.298
r_scangle_other	5.236
r_scangle_it	5.234
r_mcangle_it	3.843
r_mcangle_other	3.843
r_scbond_it	3.598
r_scbond_other	3.592
r_mcbond_it	2.993
r_mcbond_other	2.989
r_angle_other_deg	2.3
r_angle_refined_deg	1.57
r_symmetry_nbd_other	0.21
r_symmetry_nbd_refined	0.209
r_nbd_other	0.207
r_nbd_refined	0.205
r_symmetry_xyhbond_nbd_refined	0.181
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.159
r_chiral_restr	0.073
r_symmetry_nbtor_other	0.069
r_symmetry_xyhbond_nbd_other	0.061
r_bond_other_d	0.035
r_gen_planes_other	0.01
r_bond_refined_d	0.009
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5565
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	72

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing