Experiment: 9L62

A novel allosteric covalent inhibitory site of fucosyltransferase 8 revealed by crystal structures

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6X5S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291.15	0.02M Xylitol, 0.02M Myo-Inositol, 0.02M D-(-)- Fructose, 0.02M L-Rhamnose monohydrate, 0.02M D-Sorbitol, 0.1 M MOPSO, 0.1 M Bis-Tris pH 6.5, 10% w/v PEG 8000 and 20% v/v 1,5-Pentanediol

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 193.626	α = 90
b = 68.831	β = 132.67
c = 142.553	γ = 90

Symmetry
Space Group	C 1 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	STFC Large Pixel Detector		2023-06-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97918	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	3.04	96.81	97.5	0.092	0.865	6.1	3.1		26322

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.04	3.2			0.426	0.837

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	3.04	52.41	1.37	26150	1983	96.77	0.2193	0.2145	0.2158	0.2764	0.2766

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	7.397
f_angle_d	1.283
f_chiral_restr	0.064
f_bond_d	0.012
f_plane_restr	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7328
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	34

Software

Software
Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
autoPROC	data reduction
MOLREP	phasing