7G7M | pdb_00007g7m

Crystal Structure of rat Autotaxin in complex with N-[(3,4-dichlorophenyl)methyl]-N-methyl-2-[4-oxo-6-[4-(1,3-thiazol-2-yl)piperazin-1-yl]quinazolin-3-yl]acetamide, i.e. SMILES N1=C(SC=C1)N1CCN(CC1)c1ccc2N=CN(CC(=O)N(C)Cc3ccc(c(c3)Cl)Cl)C(=O)c2c1 with IC50=0.0764342 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
2.39	48.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.073	α = 90
b = 91.82	β = 90
c = 120.696	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		2015-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.999930	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	1.69	45.91	96.2	0.132	0.145	0.993	6.26	5.527		100434			36.466

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	1.69	1.74	84.7		2.59	2.891	0.593	0.62	4.887

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	1.69	45.91	40062	2192	40.51	0.1952	0.1918	0.1919	0.2561	0.2562	RANDOM	32.606

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]
-1.35			0.32		1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.776
r_dihedral_angle_4_deg	17.135
r_dihedral_angle_3_deg	15.309
r_dihedral_angle_1_deg	12.054
r_mcangle_it	2.931
r_scbond_it	2.003
r_mcbond_it	1.723
r_angle_refined_deg	1.468
r_chiral_restr	0.106
r_bond_refined_d	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.776
r_dihedral_angle_4_deg	17.135
r_dihedral_angle_3_deg	15.309
r_dihedral_angle_1_deg	12.054
r_mcangle_it	2.931
r_scbond_it	2.003
r_mcbond_it	1.723
r_angle_refined_deg	1.468
r_chiral_restr	0.106
r_bond_refined_d	0.01
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6500
Nucleic Acid Atoms
Solvent Atoms	471
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.