5E88 | pdb_00005e88

Crystal structure of Human galectin-3 CRD in complex with thienyl-1,2,3-triazolyl thiodigalactoside 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
2.14	42.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.464	α = 90
b = 58.034	β = 90
c = 63.122	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		2009-05-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	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	1.599	42.722	99.5	0.04	0.043	0.015	22.5	5.8	18255	18255

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	1.6	1.69	97		0.205	0.205	0.149	3.7	2.7	2522

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	1.6	42.72	17245	928	99.13	0.1601	0.1592	0.16	0.1783	0.18	RANDOM	18.859

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]
0.24			-0.02		-0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.003
r_dihedral_angle_3_deg	11.862
r_dihedral_angle_4_deg	9.364
r_dihedral_angle_1_deg	6.36
r_mcangle_it	2.084
r_angle_refined_deg	1.647
r_mcbond_it	1.447
r_mcbond_other	1.446
r_angle_other_deg	0.682
r_chiral_restr	0.075

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.003
r_dihedral_angle_3_deg	11.862
r_dihedral_angle_4_deg	9.364
r_dihedral_angle_1_deg	6.36
r_mcangle_it	2.084
r_angle_refined_deg	1.647
r_mcbond_it	1.447
r_mcbond_other	1.446
r_angle_other_deg	0.682
r_chiral_restr	0.075
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
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	146
Heterogen Atoms	42

Software

Software
Software Name	Purpose
SAINT	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	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.