5DUV | pdb_00005duv

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

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	7.2	293.15	0.2 M calcium acetate, 20 % w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.92	α = 90
b = 64.75	β = 91.26
c = 64.47	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 210r		2013-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.9537	Australian Synchrotron	MX1

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	1.9	37.24	98.1	0.078	0.044	0.997	12.2	4		40168

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	1.9	1.94	82.1		0.267	0.177	0.898	4.1	3.2	2128

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	1.9	37.24	38075	2016	97.89	0.1574	0.1552	0.17	0.1987	0.2	RANDOM	17.307

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]
-0.17		0.1	0.74		-0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.216
r_dihedral_angle_3_deg	14.587
r_dihedral_angle_4_deg	13.055
r_dihedral_angle_1_deg	7.023
r_mcangle_it	2.52
r_mcbond_it	1.74
r_mcbond_other	1.731
r_angle_refined_deg	1.063
r_angle_other_deg	0.514
r_chiral_restr	0.064

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.216
r_dihedral_angle_3_deg	14.587
r_dihedral_angle_4_deg	13.055
r_dihedral_angle_1_deg	7.023
r_mcangle_it	2.52
r_mcbond_it	1.74
r_mcbond_other	1.731
r_angle_refined_deg	1.063
r_angle_other_deg	0.514
r_chiral_restr	0.064
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4408
Nucleic Acid Atoms
Solvent Atoms	380
Heterogen Atoms	104

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.