7G3T | pdb_00007g3t

Crystal Structure of rat Autotaxin in complex with (2S)-6-chloro-2-[[5-(6-oxa-1-azaspiro[3.3]heptane-1-carbonyl)pyrimidin-2-yl]amino]-2,3-dihydro-1H-indene-4-carbonitrile, i.e. SMILES C1c2cc(cc(C#N)c2C[C@H]1Nc1ncc(cn1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 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
2.37	48.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.77	α = 90
b = 91.69	β = 90
c = 120.29	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		2018-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.00004	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	1.33	72.92	97.3	0.096	0.104	0.999	10.66	7.51		206305			22.449

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	1.33	1.36	94.2		2.214	2.369	0.344	0.82	7.817

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	1.33	72.92	194165	10352	97.42	0.1372	0.1353	0.1355	0.1715	0.1714	RANDOM	21.53

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]
-0.17			0.05		0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.223
r_dihedral_angle_1_deg	25.736
r_sphericity_free	21.58
r_dihedral_angle_4_deg	16.018
r_sphericity_bonded	15.375
r_dihedral_angle_3_deg	13.04
r_mcangle_it	3.232
r_rigid_bond_restr	2.778
r_mcbond_it	2.493
r_mcbond_other	2.481

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.223
r_dihedral_angle_1_deg	25.736
r_sphericity_free	21.58
r_dihedral_angle_4_deg	16.018
r_sphericity_bonded	15.375
r_dihedral_angle_3_deg	13.04
r_mcangle_it	3.232
r_rigid_bond_restr	2.778
r_mcbond_it	2.493
r_mcbond_other	2.481
r_angle_refined_deg	1.633
r_angle_other_deg	1.055
r_chiral_restr	0.092
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6509
Nucleic Acid Atoms
Solvent Atoms	868
Heterogen Atoms	139

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.