1ON6 | pdb_00001on6

Crystal structure of mouse alpha-1,4-N-acetylhexosaminotransferase (EXTL2) in complex with UDPGlcNAc

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OMX	Apo enzyme pdb:1OMX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	PEG3000, mgcl2, cacodyltate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.064	α = 90
b = 126.064	β = 90
c = 83.936	γ = 90

Symmetry
Space Group	P 4 21 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	IMAGE PLATE	RIGAKU RAXIS IV	mirrors	2002-03-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (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	2.3	50	91.1	0.064	23.2	8.9		27856	-3	-3	19.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.38	72.9		0.299	3.3	3.9	2184

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Apo enzyme pdb:1OMX	2.3	19.93	28944	27600	1344	90.3	0.198	0.196	0.196	0.19	0.234	0.22	RANDOM	34.7

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]
0.75			0.75		-1.51

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24
c_scangle_it	2.83
c_mcangle_it	2.41
c_scbond_it	1.99
c_mcbond_it	1.44
c_angle_deg	1.2
c_improper_angle_d	0.83
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4040
Nucleic Acid Atoms
Solvent Atoms	202
Heterogen Atoms	88

Software

Software
Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
CNS	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.