6L68 | pdb_00006l68

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

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
2.69	54.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.9	α = 90
b = 48.9	β = 90
c = 259.68	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		2018-11-30	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	1.92	19.61	97.7	0.999	18.7	19.9		14791

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	1.92	1.97			0.911

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1QKQ	1.92	19.607	14791	747	97.714	0.182	0.1804	0.19	0.2093	0.22	18.009

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]
0.015	0.007		0.015		-0.048

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.643
r_dihedral_angle_4_deg	20.763
r_dihedral_angle_3_deg	13.495
r_dihedral_angle_1_deg	8.319
r_lrange_other	4.599
r_lrange_it	4.592
r_scangle_it	3.42
r_scangle_other	3.418
r_scbond_it	2.098
r_scbond_other	2.098
r_mcangle_it	1.924
r_mcangle_other	1.923
r_angle_refined_deg	1.469
r_mcbond_it	1.228
r_mcbond_other	1.22
r_angle_other_deg	1.214
r_nbd_refined	0.179
r_nbd_other	0.173
r_symmetry_nbd_other	0.164
r_symmetry_xyhbond_nbd_refined	0.164
r_nbtor_refined	0.159
r_xyhbond_nbd_refined	0.094
r_symmetry_nbtor_other	0.075
r_symmetry_nbd_refined	0.072
r_chiral_restr	0.063
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1130
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms	24

Software

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