7G2W | pdb_00007g2w

Crystal Structure of rat Autotaxin in complex with 4-[3-[(2-tert-butyl-4-chloro-5-methylphenyl)methoxy]-4,5,7,8-tetrahydro-1H-pyrazolo[3,4-d]azepine-6-carbonyl]benzenesulfonamide, i.e. SMILES c1(ccc(cc1)C(=O)N1CCC2=C(CC1)NN=C2OCc1c(cc(c(c1)C)Cl)C(C)(C)C)S(=O)(=O)N with IC50=0.0150328 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
2.22	44.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.95	α = 90
b = 90.58	β = 90
c = 116.49	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		2016-04-06	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	1.25	48.99	98.5	0.066	0.071	1	13.72	6.633		235120			21.106

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	1.25	1.28	95.9		2.044	2.221	0.331	0.83	6.433

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	1.25	48.99	213224	11109	93.99	0.1341	0.1323	0.1324	0.1689	0.1689	RANDOM	21.603

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]
-0.43			0.56		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.15
r_sphericity_free	19.07
r_dihedral_angle_4_deg	16.882
r_dihedral_angle_3_deg	12.636
r_sphericity_bonded	10.035
r_dihedral_angle_1_deg	6.564
r_rigid_bond_restr	4.416
r_mcangle_it	3.126
r_mcbond_it	2.621
r_mcbond_other	2.605

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.15
r_sphericity_free	19.07
r_dihedral_angle_4_deg	16.882
r_dihedral_angle_3_deg	12.636
r_sphericity_bonded	10.035
r_dihedral_angle_1_deg	6.564
r_rigid_bond_restr	4.416
r_mcangle_it	3.126
r_mcbond_it	2.621
r_mcbond_other	2.605
r_angle_refined_deg	2.134
r_angle_other_deg	1.367
r_chiral_restr	0.146
r_bond_refined_d	0.023
r_gen_planes_refined	0.012
r_gen_planes_other	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6369
Nucleic Acid Atoms
Solvent Atoms	796
Heterogen Atoms	181

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.