6L6D

X-ray structure of human galectin-10 in complex with D-N-acetylgalactosamine

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
2.71	54.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.9	α = 90
b = 48.9	β = 90
c = 261.66	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		2019-08-28	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	1.93	19.63	99.8	0.998	16.8	19.3		14992

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	1.93	1.98			0.903

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	1.93	19.628	14992	759	99.814	0.203	0.2017	0.2332	17.848

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		-0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.522
r_dihedral_angle_4_deg	22.931
r_dihedral_angle_3_deg	17.407
r_dihedral_angle_1_deg	9.076
r_lrange_it	3.915
r_lrange_other	3.915
r_scangle_it	2.653
r_scangle_other	2.651
r_mcangle_it	1.78
r_mcangle_other	1.779
r_scbond_it	1.635
r_scbond_other	1.634
r_angle_refined_deg	1.363
r_angle_other_deg	1.189
r_mcbond_it	1.068
r_mcbond_other	1.068
r_nbd_refined	0.17
r_symmetry_nbd_other	0.165
r_nbtor_refined	0.159
r_symmetry_xyhbond_nbd_refined	0.155
r_nbd_other	0.154
r_xyhbond_nbd_refined	0.12
r_symmetry_nbd_refined	0.083
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.057
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	70
Heterogen Atoms	15

Software

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