6L6B

X-ray structure of human galectin-10 in complex with L-fucose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QKQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	1.6 M ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10 % (v/v) 1,4-dioxane

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.82	α = 90
b = 48.82	β = 90
c = 261.03	γ = 120

Symmetry
Space Group	P 65 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU		2018-10-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	1.8	19.55	99.5	0.997	15.1	18.6		18129

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	1.8	1.85			0.977

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	1QKQ	1.802	19.546	18129	926	99.544	0.215	0.2126	0.2553	16.868

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]
0.046	0.023		0.046		-0.148

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.19
r_dihedral_angle_4_deg	19.101
r_dihedral_angle_3_deg	14.607
r_dihedral_angle_1_deg	9.106
r_lrange_it	3.625
r_lrange_other	3.617
r_scangle_it	2.396
r_scangle_other	2.394
r_mcangle_it	1.595
r_mcangle_other	1.594
r_scbond_it	1.484
r_scbond_other	1.483
r_angle_refined_deg	1.419
r_angle_other_deg	1.21
r_mcbond_it	0.982
r_mcbond_other	0.982
r_nbd_refined	0.171
r_symmetry_nbd_other	0.162
r_nbtor_refined	0.16
r_nbd_other	0.157
r_symmetry_xyhbond_nbd_refined	0.151
r_xyhbond_nbd_refined	0.128
r_symmetry_nbd_refined	0.098
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.072
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1159
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms	11

Software

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