9L6E | pdb_00009l6e

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, HANGING DROP		291.15	0.02M DL-Arginine hydrochloride, 0.02M DL-Threonine, 0.02M DL-Histidine monohydrochloride monohydrate, 0.02M DL-5-Hydroxylysine hydrochloride, 0.02M trans-4-hydroxy-L-proline, 0.1 M MOPSO, 0.1 M Bis-Tris pH 6.5, 15% w/v PEG 3000, 20% v/v 1, 2, 4-Butanetriol and 2% w/v NDSB 256.

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 192.79	α = 90
b = 67.91	β = 132.15
c = 140.82	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		2024-04-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.97918	SSRF	BL10U2

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	3.07	71.46	99.5	0.175	0.994	8.6	3.2		25445

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	3.07	3.15			0.992	0.744	1.8

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	3.07	71.46	1.35	25404	1239	99.32	0.2326	0.2287	0.2486	0.3105	0.3062

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	7.49
f_angle_d	1.155
f_chiral_restr	0.058
f_plane_restr	0.014
f_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7245
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	91

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
MOLREP	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.