7G53 | pdb_00007g53

Crystal Structure of rat Autotaxin in complex with 1H-benzotriazol-5-yl-[rac-(1R,2S,6R,7S)-9-[4-(2-methoxyethoxy)quinoline-2-carbonyl]-4,9-diazatricyclo[5.3.0.02,6]decan-4-yl]methanone, i.e. SMILES N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)c1ccc2c(c1)N=NN2)C(=O)c1nc2c(c(c1)OCCOC)cccc2 with IC50=0.223388 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
2.38	48.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.101	α = 90
b = 91.98	β = 90
c = 119.696	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		2013-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000000	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	1.73	45.99	99.9	0.105	0.114	0.998	11.44	6.648		97372			30.12

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	1.73	1.77	99.9		1.316	1.435	0.506	1.32	6.226

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	1.73	45.99	89123	4792	96.47	0.1858	0.184	0.1829	0.2204	0.2193	RANDOM	26.572

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]
-0.56			0.22		0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.732
r_dihedral_angle_4_deg	14.832
r_dihedral_angle_3_deg	13.486
r_dihedral_angle_1_deg	6.349
r_angle_refined_deg	1.712
r_chiral_restr	0.123
r_bond_refined_d	0.016
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6508
Nucleic Acid Atoms
Solvent Atoms	563
Heterogen Atoms	141

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.