3AP7 | pdb_00003ap7

Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with lactose sialic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3AP5	PDB ENTRY 3AP5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293.15	0.275mM protein, 10mM Hepes-NaOH, 2.75mM lactose sialic acid, 50mM sodium chloride, 0.5mM DTT, 80mM ammonium fluoride, 7.5% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.36	α = 90
b = 49.917	β = 90
c = 70.289	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	95	CCD	ADSC QUANTUM 315r		2005-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.000000	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.53	24.961	99.9	0.034	0.034		12.8	25280	25280			14.014

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.53	1.57	100		0.192	0.192	12.4	8.5	1826

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB ENTRY 3AP5	1.53	24.96	23937	23937	1282	100	0.16493	0.16493	0.16373	0.18	0.18828	0.19	RANDOM	11.776

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]
0.53			-0.13		-0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.027
r_dihedral_angle_4_deg	19.095
r_dihedral_angle_3_deg	10.596
r_dihedral_angle_1_deg	6.593
r_scangle_it	2.9
r_scbond_it	1.812
r_mcangle_it	1.328
r_angle_refined_deg	1.299
r_angle_other_deg	0.794
r_mcbond_it	0.739

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.027
r_dihedral_angle_4_deg	19.095
r_dihedral_angle_3_deg	10.596
r_dihedral_angle_1_deg	6.593
r_scangle_it	2.9
r_scbond_it	1.812
r_mcangle_it	1.328
r_angle_refined_deg	1.299
r_angle_other_deg	0.794
r_mcbond_it	0.739
r_mcbond_other	0.155
r_chiral_restr	0.083
r_bond_refined_d	0.009
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	1204
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	44

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.