5DLW

Crystal structure of Autotaxin (ENPP2) with tauroursodeoxycholic acid (TUDCA) and lysophosphatidic acid (LPA)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	20% PEG 3350, 0.3M sodium thiocyanate, 0.2M sodium iodide, 350 uM TUDCA, 100 uM LPA

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.197	α = 90
b = 93.051	β = 90
c = 149.68	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	PIXEL	DECTRIS PILATUS 6M-F		2015-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97626	ESRF	ID29

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	1.8	46.53	99.8	0.165	0.074	0.995	8.6	5.9		82325

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	1.8	1.83	99.3		2.551	1.14	0.259	1	5.8	4435

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	79.03	78197	4048	99.66	0.1893	0.1879	0.2163	RANDOM	32.905

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]
-0.22			0.58		-0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	54.574
r_sphericity_bonded	50.99
r_dihedral_angle_2_deg	34.002
r_dihedral_angle_4_deg	17.274
r_dihedral_angle_3_deg	11.542
r_dihedral_angle_1_deg	6.424
r_mcangle_it	2.945
r_mcbond_it	1.924
r_mcbond_other	1.924
r_angle_refined_deg	1.466

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	54.574
r_sphericity_bonded	50.99
r_dihedral_angle_2_deg	34.002
r_dihedral_angle_4_deg	17.274
r_dihedral_angle_3_deg	11.542
r_dihedral_angle_1_deg	6.424
r_mcangle_it	2.945
r_mcbond_it	1.924
r_mcbond_other	1.924
r_angle_refined_deg	1.466
r_angle_other_deg	1.112
r_chiral_restr	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6302
Nucleic Acid Atoms
Solvent Atoms	311
Heterogen Atoms	182

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
Coot	model building

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.