5EXO | pdb_00005exo

Crystal structure of Human galectin-3 CRD in complex with methyl 2-O-acetyl-3-O-(2H-chromene-3-yl-methyl)-a-D-galactopyranoside inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NN8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	31% PEG 6000, 100MM MGCL2, 8MM BETA MERCEPTOETHANOL, 100MM TRIS HCL

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.796	α = 90
b = 58.411	β = 90
c = 63.928	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	CCD	BRUKER SMART 6000		2010-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	MACSCIENCE	1.54184

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	1.502	43.122	95	0.053	0.057	0.019	16.3	5.2	21563	21563

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	1.5	1.58	65.7		0.257	0.257	0.226	3	1.6	2108

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	2nn8	1.502	43.12	20351	1100	94.71	0.1586	0.1568	0.16	0.1928	0.19	RANDOM	17.641

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]
0.58			-0.43		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.912
r_dihedral_angle_4_deg	13.886
r_dihedral_angle_3_deg	10.452
r_dihedral_angle_1_deg	6.804
r_scangle_it	5.525
r_scbond_it	3.591
r_mcangle_it	3.185
r_mcbond_it	1.915
r_angle_refined_deg	1.42
r_angle_other_deg	0.805

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.912
r_dihedral_angle_4_deg	13.886
r_dihedral_angle_3_deg	10.452
r_dihedral_angle_1_deg	6.804
r_scangle_it	5.525
r_scbond_it	3.591
r_mcangle_it	3.185
r_mcbond_it	1.915
r_angle_refined_deg	1.42
r_angle_other_deg	0.805
r_mcbond_other	0.454
r_chiral_restr	0.093
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1101
Nucleic Acid Atoms
Solvent Atoms	164
Heterogen Atoms	29

Software

Software
Software Name	Purpose
SAINT	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building

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.