9FYJ | pdb_00009fyj

N-terminal domain of human galectin-8 in complex with an alpha-galactoside ligand

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		in-house galectin-8N structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	Drops consisted of 2 ul galectin-8N at 13.1 mg/ml in PBS buffer, 1 mM ligand, 5% DMSO mixed with 2 ul of reservoir solution consisting of 35% (w/v) Morpheus precipitant mix 4, 0.16 M Morpheus alcohol mix, 61 mM MES, 39 mM imidazole, pH 7.5. Morpheus precipitant mix 4 is made up of 25% (w/v) each of methane pentane diol (MPD), polyethylene glycol (PEG) 1000 and PEG 3350. Morpheus alcohol mix contains 0.2 M each of 1,6-hexanediol, 1-butanol, 1,2-propanediol, 2-propanol, 1,4-butanediol and 1,3-propanediol (1.2 M total).

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.689	α = 90
b = 62.28	β = 90
c = 84.791	γ = 90

Symmetry
Space Group	P 21 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		2023-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.8000	MAX IV	BioMAX

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	1.08	45.4	98	0.054	0.056	0.015	0.999	18.4	12.4		119679			14.56

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	1.08	1.12	83.8		1.465	1.573	0.554	0.559	1.2	7.7

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.08	42.4	1.34	119551	5966	97.8	0.1333	0.1324	0.1486	0.1503	0.1608	RANDOM	20.64

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	13.198
f_angle_d	1.0343
f_chiral_restr	0.0935
f_plane_restr	0.0112
f_bond_d	0.0081

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2377
Nucleic Acid Atoms
Solvent Atoms	378
Heterogen Atoms	75

Software

Software
Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
EDNA	data collection
PHASER	phasing