5DUU | pdb_00005duu

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

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
1.89	34.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.238	α = 90
b = 64.533	β = 90.88
c = 64.685	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		2014-03-19	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	45.68	99.5	0.074	0.039	0.998	15.8	4.5		35098

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	2.05	97.4		0.279	0.149	0.943	5.2	4.3	2534

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	2	45.68	33349	1732	99.46	0.1858	0.1839	0.19	0.2219	0.23	RANDOM	18.537

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]
-0.82		-0.16	1.61		-0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.215
r_dihedral_angle_4_deg	16.493
r_dihedral_angle_3_deg	14.507
r_dihedral_angle_1_deg	6.564
r_mcangle_it	1.845
r_angle_other_deg	1.35
r_angle_refined_deg	1.344
r_mcbond_it	1.1
r_mcbond_other	1.099
r_chiral_restr	0.069

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.215
r_dihedral_angle_4_deg	16.493
r_dihedral_angle_3_deg	14.507
r_dihedral_angle_1_deg	6.564
r_mcangle_it	1.845
r_angle_other_deg	1.35
r_angle_refined_deg	1.344
r_mcbond_it	1.1
r_mcbond_other	1.099
r_chiral_restr	0.069
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4423
Nucleic Acid Atoms
Solvent Atoms	306
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
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.