4YM3 | pdb_00004ym3

Crystal structure of the human galectin-4 C-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	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 pH 7.0, 4 % v/v PEG 400

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.533	α = 90
b = 130.185	β = 96.91
c = 45.465	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		2013-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9713	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.889	65.092	98.9	0.195	0.202	0.053	15.8	12.1	41495	41495

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.87	1.98	91.5		0.515	0.515	0.201	1.1	7.1	4717

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	1.89	45.2	39334	2127	98.85	0.1688	0.1674	0.17	0.1959	0.19	RANDOM	20.778

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]
-1.83		3.34	9.01		-7.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.042
r_dihedral_angle_3_deg	13.751
r_dihedral_angle_4_deg	12.179
r_dihedral_angle_1_deg	6.687
r_mcangle_it	1.379
r_angle_refined_deg	1.296
r_angle_other_deg	0.849
r_mcbond_it	0.778
r_mcbond_other	0.778
r_chiral_restr	0.072

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.042
r_dihedral_angle_3_deg	13.751
r_dihedral_angle_4_deg	12.179
r_dihedral_angle_1_deg	6.687
r_mcangle_it	1.379
r_angle_refined_deg	1.296
r_angle_other_deg	0.849
r_mcbond_it	0.778
r_mcbond_other	0.778
r_chiral_restr	0.072
r_bond_refined_d	0.006
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	4357
Nucleic Acid Atoms
Solvent Atoms	329
Heterogen Atoms	92

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	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.