2NN8 | pdb_00002nn8

Crystal structure of human galectin-3 carbohydrate-recognition domain with lactose bound, at 1.35 angstrom resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1A3K	PDB ENTRY 1A3K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	31% PEG 6000, 100mM MgCL2, 8mM beta mercaptoethanol, 100mM Tris-HCL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.371	α = 90
b = 57.8	β = 90
c = 62.603	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	100	CCD	ADSC QUANTUM 4		2005-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.1159	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.35	42.49	98.3	0.036	11.5	3.7	29182	29182

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35	1.42	89.9		0.21	3.4

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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1A3K	1.35	27.62	27660	1482	98.13	0.16476	0.16418	0.16	0.1749	0.17	RANDOM	13.881

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]
0.31			-0.28		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.122
r_dihedral_angle_4_deg	12.995
r_dihedral_angle_3_deg	11.753
r_dihedral_angle_1_deg	6.554
r_scangle_it	4.118
r_scbond_it	2.757
r_mcangle_it	1.989
r_mcbond_it	1.437
r_angle_refined_deg	1.287
r_nbtor_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.122
r_dihedral_angle_4_deg	12.995
r_dihedral_angle_3_deg	11.753
r_dihedral_angle_1_deg	6.554
r_scangle_it	4.118
r_scbond_it	2.757
r_mcangle_it	1.989
r_mcbond_it	1.437
r_angle_refined_deg	1.287
r_nbtor_refined	0.31
r_nbd_refined	0.193
r_symmetry_vdw_refined	0.147
r_symmetry_hbond_refined	0.109
r_xyhbond_nbd_refined	0.093
r_chiral_restr	0.089
r_bond_refined_d	0.007
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1108
Nucleic Acid Atoms
Solvent Atoms	197
Heterogen Atoms	53

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	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.