4YLZ | pdb_00004ylz

Crystal structure of the human galectin-4 C-terminal carbohydrate recognition domain in complex with lacto-N-neotetraose (LNnT)

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293.15	1.2 M ammonium sulfate, 0.1 M HEPES, 4 % v/v PEG 400

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.083	α = 90
b = 127.64	β = 96.05
c = 45.102	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	2.1	44.85	99.8	0.094	0.038	0.996	19.5	5.6		29532

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	2.1	2.16	99.8		0.139	0.08	0.959	14.6	4	2449

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	3OJB	2.1	44.85	28099	1403	99.82	0.2082	0.2055	0.21	0.2654	0.27	RANDOM	25.471

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]
-0.61		0.07	1.26		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.731
r_dihedral_angle_3_deg	15.38
r_dihedral_angle_4_deg	11.174
r_dihedral_angle_1_deg	6.868
r_mcangle_it	2.228
r_angle_refined_deg	1.355
r_mcbond_it	1.283
r_mcbond_other	1.281
r_angle_other_deg	0.873
r_chiral_restr	0.073

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.731
r_dihedral_angle_3_deg	15.38
r_dihedral_angle_4_deg	11.174
r_dihedral_angle_1_deg	6.868
r_mcangle_it	2.228
r_angle_refined_deg	1.355
r_mcbond_it	1.283
r_mcbond_other	1.281
r_angle_other_deg	0.873
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4350
Nucleic Acid Atoms
Solvent Atoms	142
Heterogen Atoms	228

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	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.