4YM2 | pdb_00004ym2

Crystal structure of the human galectin-4 C-terminal carbohydrate recognition domain in complex with lactose-3'-sulfate

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
2.12	36.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.224	α = 90
b = 129.208	β = 96.88
c = 45.233	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	44.91	98.4	0.111	0.045	0.995	12.5	5.5		29564

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	96.8		0.181	0.107	0.89	6.4	3.7	2426

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	42.42	28144	1388	98.21	0.163	0.1607	0.17	0.2103	0.22	RANDOM	28.064

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]
-4.48		6.25	3.51		0.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.802
r_dihedral_angle_3_deg	15.063
r_dihedral_angle_4_deg	13.066
r_dihedral_angle_1_deg	7.029
r_mcangle_it	2.004
r_angle_refined_deg	1.346
r_angle_other_deg	1.223
r_mcbond_it	1.127
r_mcbond_other	1.127
r_chiral_restr	0.101

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.802
r_dihedral_angle_3_deg	15.063
r_dihedral_angle_4_deg	13.066
r_dihedral_angle_1_deg	7.029
r_mcangle_it	2.004
r_angle_refined_deg	1.346
r_angle_other_deg	1.223
r_mcbond_it	1.127
r_mcbond_other	1.127
r_chiral_restr	0.101
r_bond_refined_d	0.007
r_bond_other_d	0.005
r_gen_planes_refined	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4350
Nucleic Acid Atoms
Solvent Atoms	149
Heterogen Atoms	100

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.