Experiment: 8UJH

X-ray crystal structure of Toxoplasma gondii GalNAc-T3 in complex with UDP-GalNAc, Mn2+, and a CST1 diglycopeptide.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8UHV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9.5	293	0.1 M CHES pH 9.5 and 14-20% PEG 8000 (w/v)

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.722	α = 90
b = 66.833	β = 90
c = 166.047	γ = 90

Symmetry
Space Group	P 2 21 21

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	FMB OXFORD dual crystal DCM; IDT KB Mirror system	2022-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1	APS	22-ID

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	2.65	30	99.6	0.29	0.314	0.12	0.949	7.56	6.5		20609			46.83

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.65	2.7	96		1.557	1.771	0.822	0.36	0.93	4.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.65	29.74	1.36	20556	1006	99.37	0.1918	0.1895	0.1901	0.2338	0.2344	51.18

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.1828
f_angle_d	0.5133
f_chiral_restr	0.0401
f_plane_restr	0.0042
f_bond_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4247
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms	47

Software

Software
Software Name	Purpose
PHENIX	refinement
SERGUI	data collection
Aimless	data scaling
MOLREP	phasing
HKL-2000	data collection