7G5Y | pdb_00007g5y

Crystal Structure of rat Autotaxin in complex with 3-[[4-chloro-5-methyl-2-[3-(morpholine-4-carbonyl)phenyl]phenoxy]methyl]-4-methyl-1H-1,2,4-triazol-5-one, i.e. SMILES c1c(c(cc(c1c1cccc(c1)C(=O)N1CCOCC1)OCC1=NNC(=O)N1C)C)Cl with IC50=0.130955 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
2.36	47.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.035	α = 90
b = 91.893	β = 90
c = 119.102	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		2013-08-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.999970	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	1.52	42.87	100	0.089	0.097	0.999	11.48	6.625		141984			28.458

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	1.52	1.56	100		1.995	2.165	0.352	0.94	6.639

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	1.52	42.87	129019	6861	95.73	0.1561	0.1537	0.1534	0.2027	0.2025	RANDOM	27.303

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]
-0.18			-0.29		0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.991
r_sphericity_free	20.755
r_dihedral_angle_4_deg	14.507
r_dihedral_angle_3_deg	12.582
r_sphericity_bonded	11.637
r_dihedral_angle_1_deg	6.244
r_scbond_it	3.9
r_rigid_bond_restr	3.819
r_mcangle_it	3.362
r_mcbond_it	2.841

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.991
r_sphericity_free	20.755
r_dihedral_angle_4_deg	14.507
r_dihedral_angle_3_deg	12.582
r_sphericity_bonded	11.637
r_dihedral_angle_1_deg	6.244
r_scbond_it	3.9
r_rigid_bond_restr	3.819
r_mcangle_it	3.362
r_mcbond_it	2.841
r_angle_refined_deg	1.505
r_chiral_restr	0.106
r_bond_refined_d	0.013
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6500
Nucleic Acid Atoms
Solvent Atoms	621
Heterogen Atoms	144

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.