6W4Z

Galectin-8N terminal domain in complex with Methyl 3-O-[3-O-benzyloxy]-malonyl-beta-D-galactopyranoside

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5T7S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298.15	0.1M sodium citrate dihydrate pH 5.6, 20% PEG 4000, 10% IPA

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.391	α = 90
b = 40.003	β = 98.222
c = 70.324	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	CCD	ADSC QUANTUM 315r		2019-03-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

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	1.59	46.32	99.9	0.116	0.997	8.8	6.8		41190

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.59	1.62	99.7		1.538	0.946	0.805		6.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5T7S	1.59	46.31	41186	2139	99.91	0.194	0.1925	0.2255	19.814

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]
		-0.001	0.001		-0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.949
r_dihedral_angle_4_deg	20.393
r_dihedral_angle_3_deg	14.68
r_lrange_it	7.551
r_lrange_other	7.551
r_dihedral_angle_1_deg	7.176
r_scangle_it	4.561
r_scangle_other	4.56
r_scbond_it	3.023
r_scbond_other	3.022
r_mcangle_other	2.584
r_mcangle_it	2.582
r_angle_refined_deg	1.837
r_mcbond_it	1.781
r_mcbond_other	1.774
r_angle_other_deg	1.405
r_chiral_restr_other	1.169
r_nbd_other	0.287
r_symmetry_nbd_refined	0.285
r_symmetry_xyhbond_nbd_refined	0.262
r_nbd_refined	0.223
r_symmetry_nbd_other	0.186
r_xyhbond_nbd_refined	0.173
r_nbtor_refined	0.168
r_chiral_restr	0.081
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2432
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	74

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing