9FXZ | pdb_00009fxz

Galectin-8 N-terminal carbohydrate recognition domain in complex with 4-(bromophenyl)phthalazinone D-galactal ligand

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5GZD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293.5	A co-crystal with lactose, grown from 12 mg/ml galectin-8N in 10 mM lactose, 10 mM Tris/HCl pH 8.0, 1 mM TCEP and 150 mM sodium chloride mixed with 25% (w/v) PEG 2000 MME) in a hanging drop, was used to soak the compound by transferring crystals in three steps to soaking drops. These were 2 uL drops with a soaking solution of 20% ethylene glycol, 25% PEG 2000 MME, 10 mM Tris pH 8, 1 mM TCEP, 50 mM NaCl, and 2 mM compound 10. The incubation times in the first two drops were about 10 min and in the third drop about 24 h. Then the crystals were transferred to a cryo solution with the same constituents and flash-frozen in liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.71	α = 90
b = 62.28	β = 90
c = 84.75	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 PILATUS3 X 6M	Oxford Danfysik/SESO Two stage demagnification using two K-B pairs of bimorph type mirrors	2021-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.99990	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.3	46.01	99.8	0.998	12.5	6.2		71690

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.32	99.9		0.593	1.1	5.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.3	46.007	71690	3642	99.729	0.159	0.1572	0.1567	0.2003	0.2001	23.87

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]
0.476			0.253		-0.729

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	18.332
r_lrange_other	18.132
r_dihedral_angle_6_deg	14.743
r_scangle_it	11.92
r_scangle_other	11.917
r_dihedral_angle_3_deg	11.769
r_mcangle_other	9.138
r_mcangle_it	9.127
r_scbond_it	9.07
r_scbond_other	9.066
r_dihedral_angle_1_deg	7.336
r_mcbond_it	7.287
r_mcbond_other	7.244
r_dihedral_angle_2_deg	6.44
r_rigid_bond_restr	5.218
r_angle_refined_deg	1.793
r_angle_other_deg	0.634
r_symmetry_nbd_refined	0.253
r_nbd_other	0.209
r_nbd_refined	0.202
r_symmetry_nbd_other	0.2
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.166
r_symmetry_xyhbond_nbd_refined	0.152
r_ncsr_local_group_1	0.124
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2352
Nucleic Acid Atoms
Solvent Atoms	288
Heterogen Atoms	59

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building