7G7D | pdb_00007g7d

Crystal Structure of rat Autotaxin in complex with 5-[3-oxo-3-[rac-(3aR,8aS)-6-[2-cyclopropyl-6-(oxan-4-ylmethoxy)pyridine-4-carbonyl]-1,3,3a,4,5,7,8,8a-octahydropyrrolo[3,4-d]azepin-2-yl]propyl]-3H-1,3-oxazol-2-one, i.e. SMILES C1C[C@@H]2[C@H](CCN1C(=O)c1cc(nc(c1)OCC1CCOCC1)C1CC1)CN(C2)C(=O)CCC1=CNC(=O)O1 with IC50=0.0580555 microM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model		in house model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	293	15.3 mg/mL protein in 20mM BICINE/NaOH pH8.5, 150mM NaCl, 0.02% NaN3 mixed 50-70% with 50-30% reservoir consisting of 11-17% PEG3350, 0.1M Na-acetate pH4.5, 0.2M Ca-acetate, total volume 200nL

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.702	α = 90
b = 91.424	β = 90
c = 118.999	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	PSI PILATUS 6M		2014-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.999990	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.06	45.71	99.8	0.116	0.126	0.998	10.71	6.628		57084			47.465

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.06	2.11	99.7		2.122	2.296	0.304	0.93	6.803

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	inhouse model	2.06	45.71	51408	2759	94.79	0.1917	0.1892	0.1898	0.2372	0.2374	RANDOM	45.558

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]
-0.89			-0.72		1.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.882
r_dihedral_angle_4_deg	15.979
r_dihedral_angle_3_deg	14.248
r_dihedral_angle_1_deg	6.5
r_mcangle_it	3.927
r_scbond_it	3.815
r_mcbond_it	2.737
r_angle_refined_deg	1.561
r_chiral_restr	0.104
r_bond_refined_d	0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.882
r_dihedral_angle_4_deg	15.979
r_dihedral_angle_3_deg	14.248
r_dihedral_angle_1_deg	6.5
r_mcangle_it	3.927
r_scbond_it	3.815
r_mcbond_it	2.737
r_angle_refined_deg	1.561
r_chiral_restr	0.104
r_bond_refined_d	0.012
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6462
Nucleic Acid Atoms
Solvent Atoms	263
Heterogen Atoms	182

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	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.