7P1M

Galectin-8 N-terminal carbohydrate recognition domain in complex with benzimidazole D-galactal ligand

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	DIAMOND BEAMLINE I03
Synchrotron site	Diamond
Beamline	I03
Temperature [K]	293.5
Detector technology	PIXEL
Collection date	2019-10-22
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.97935
Spacegroup name	P 21 21 21
Unit cell lengths	54.360, 61.820, 84.590
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	49.910 - 1.520
R-factor	0.14837
Rwork	0.145
R-free	0.20737
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5gzd
RMSD bond length	0.013
RMSD bond angle	1.756
Data reduction software	XDS
Data scaling software	XDS
Phasing software	PHASER
Refinement software	REFMAC (5.8.0258)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	49.910	1.560
High resolution limit [Å]	1.520	1.520
Rmerge	0.039	1.610
Number of reflections	3108	0
<I/σ(I)>	19.1
Completeness [%]	99.9
Redundancy	6.6

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	LIQUID DIFFUSION	8	293.5	Buffer (10mM Tris/HCl pH 8.0, 150 mM NaCl, 10 mm lactose and 1 mM TCEP) mixed with reservoir 25% (w/v) PEG 2000 monomethylethyer (MME), a cryo solution (10 mM Tris/HCl pH 8.0, 50 mM NaCl, 10 mM lactose, 25% (w/v) PEG 2000 MME, 20% ethylene glycol (EG) and 1 mM TCEP) and flash-frozen in liquid nitrogen. A co-crystal with lactose, grown from a seeded drop with 24% (w/v) PEG 2000 MME in the reservoir, was used to soak in compound 1 by transferring crystals in three steps to different soaking drops. First to a 2 ul drop with glycerol ( 20% (v/v) glycerol, 25% (w/v PEG 2000 MME, 10 mM Tris/HCl pH 8.0, 50 mM NaCl and 1 mM TCEP) and secondly to a 2 ul drop with 10 mM compound 1 (10 mM Tris/HCl pH 8.0, 50 mM NaCl, 5 mM compound 1, 25% (w/v) PEG 2000 MME and 1 mM TCEP) and thirdly to a second drop with 5 mM compound 1 (same composition as before).