5DUX | pdb_00005dux

Crystal structure of the human galectin-4 N-terminal carbohydrate recognition domain in complex with 2'-fucosyllactose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3I8T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293.15	3.5 M sodium formate, 0.1 M Tris

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.152	α = 90
b = 64.469	β = 90.79
c = 64.653	γ = 90

Symmetry
Space Group	P 1 21 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		2014-07-01	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)	Rpim I (All)	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	1.85	45.65	99.1	0.041	0.024	0.998	22.9	4		44028

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	1.85	1.89	96.2		0.125	0.079	0.981	8.9	3.4	2626

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3I8T	1.85	45.65	41855	2156	98.98	0.1681	0.1662	0.18	0.2046	0.21	RANDOM	18.033

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]
-0.86		-0.01	1.59		-0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.093
r_dihedral_angle_3_deg	12.141
r_dihedral_angle_4_deg	11.434
r_dihedral_angle_1_deg	6.348
r_mcangle_it	2.588
r_mcbond_it	1.757
r_mcbond_other	1.752
r_angle_refined_deg	1.105
r_angle_other_deg	0.675
r_chiral_restr	0.064

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.093
r_dihedral_angle_3_deg	12.141
r_dihedral_angle_4_deg	11.434
r_dihedral_angle_1_deg	6.348
r_mcangle_it	2.588
r_mcbond_it	1.757
r_mcbond_other	1.752
r_angle_refined_deg	1.105
r_angle_other_deg	0.675
r_chiral_restr	0.064
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4408
Nucleic Acid Atoms
Solvent Atoms	439
Heterogen Atoms	81

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.