9FYJ

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

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	MAX IV BEAMLINE BioMAX
Synchrotron site	MAX IV
Beamline	BioMAX
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-03-06
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.8000
Spacegroup name	P 21 21 21
Unit cell lengths	53.689, 62.280, 84.791
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	42.400 - 1.080
R-factor	0.1333
Rwork	0.132
R-free	0.15030
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.008
RMSD bond angle	1.034
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX (1.21rc1_5084)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	45.400	1.120
High resolution limit [Å]	1.080	1.080
Rmerge	0.054	1.465
Rmeas	0.056	1.573
Rpim	0.015	0.554
Number of reflections	119679	9860
<I/σ(I)>	18.4	1.2
Completeness [%]	98.0	83.8
Redundancy	12.4	7.7
CC(1/2)	0.999	0.559

Crystallization Conditions

crystal 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).