7G7I | pdb_00007g7i

Crystal Structure of rat Autotaxin in complex with N-[(3-chloro-4-cyanophenyl)methyl]-2-[6-[1-(2-methoxyacetyl)piperidin-4-yl]-4-oxoquinazolin-3-yl]-N-methylacetamide, i.e. SMILES c1(ccc2c(c1)C(=O)N(C=N2)CC(=O)N(Cc1cc(c(cc1)C#N)Cl)C)C1CCN(CC1)C(=O)COC with IC50=0.0120222 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
2.45	49.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.903	α = 90
b = 92.887	β = 90
c = 121.125	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	0.999920	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	1.61	46.44	99.9	0.059	0.064	0.999	15.78	6.542		124282			37.417

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	1.61	1.65	99.9		3.402	3.696	0.354	0.6	6.563

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	1.61	46.44	113132	5882	95.77	0.2149	0.2135	0.2128	0.242	0.2417	RANDOM	32.544

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]
-1.04			0.45		0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.35
r_dihedral_angle_4_deg	14.394
r_dihedral_angle_3_deg	13.377
r_dihedral_angle_1_deg	6.339
r_mcangle_it	3.164
r_scbond_it	2.922
r_mcbond_it	2.175
r_angle_refined_deg	1.587
r_chiral_restr	0.117
r_bond_refined_d	0.015

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.35
r_dihedral_angle_4_deg	14.394
r_dihedral_angle_3_deg	13.377
r_dihedral_angle_1_deg	6.339
r_mcangle_it	3.164
r_scbond_it	2.922
r_mcbond_it	2.175
r_angle_refined_deg	1.587
r_chiral_restr	0.117
r_bond_refined_d	0.015
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6500
Nucleic Acid Atoms
Solvent Atoms	417
Heterogen Atoms	140

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.