5IJS

Crystal structure of autotaxin with orthovanadate bound as a trigonal bipyramidal intermediate analog

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5DLT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	293	Protein buffer: 4.5 mg/ml autotaxin, incubated with 1 mM orthovanadate, 20 mM hepes pH 7.4, 150 mM NaCl Crystallisation condition: 18% (w/v) PEG3350, 0.2 M NH4I, 0.4M NaSCN

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.75	α = 99.33
b = 63.45	β = 105.91
c = 70.55	γ = 99.51

Symmetry
Space Group	P 1

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 2M		2010-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.9792	SLS	X06DA

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	2.2	40	90.2	0.116	4.9	1.6		39503

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	2.2	2.32	90.7		0.825	1.4	1.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5dlt	2.2	40	37463	2000	90.06	0.2043	0.2025	0.2391	RANDOM	42.948

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]
-0.27	1.84	-0.24	-0.47	0.89	-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_bonded	45.775
r_dihedral_angle_2_deg	34.909
r_dihedral_angle_4_deg	15.983
r_dihedral_angle_3_deg	11.971
r_dihedral_angle_1_deg	6.06
r_mcangle_it	3.143
r_mcbond_it	1.962
r_mcbond_other	1.957
r_angle_refined_deg	1.231
r_angle_other_deg	0.894

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_bonded	45.775
r_dihedral_angle_2_deg	34.909
r_dihedral_angle_4_deg	15.983
r_dihedral_angle_3_deg	11.971
r_dihedral_angle_1_deg	6.06
r_mcangle_it	3.143
r_mcbond_it	1.962
r_mcbond_other	1.957
r_angle_refined_deg	1.231
r_angle_other_deg	0.894
r_chiral_restr	0.069
r_bond_refined_d	0.007
r_gen_planes_refined	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	6337
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms	68

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building
PDB-REDO	refinement

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.