7G5L | pdb_00007g5l

Crystal Structure of rat Autotaxin in complex with rac-(3aR,8aS)-6-[rac-(E)-3-[4-(trifluoromethoxy)phenyl]prop-2-enoyl]-N-(1H-triazol-5-ylmethyl)-1,3,3a,4,5,7,8,8a-octahydropyrrolo[3,4-d]azepine-2-carboxamide, i.e. SMILES c1c(ccc(c1)/C=C/C(=O)N1CC[C@@H]2[C@H](CC1)CN(C2)C(=O)NCC1=CN=NN1)OC(F)(F)F with IC50=0.493964 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
2.48	50.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.072	α = 90
b = 93.744	β = 90
c = 121.251	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		2012-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.999980	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	2.51	46.87	99.6	0.184	0.2	0.995	9.01	6.518		33750			58.578

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	2.51	2.58	99.6		1.828	1.981	0.582	1.26	6.776

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	2.51	46.87	30267	1654	94.38	0.2096	0.2067	0.2119	0.263	0.2677	RANDOM	61.397

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]
-2.37			3.3		-0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.293
r_dihedral_angle_1_deg	7.173
r_dihedral_angle_2_deg	5.119
r_mcangle_it	3.039
r_mcbond_it	1.746
r_mcbond_other	1.746
r_angle_refined_deg	1.028
r_angle_other_deg	0.346
r_chiral_restr	0.048
r_gen_planes_refined	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.293
r_dihedral_angle_1_deg	7.173
r_dihedral_angle_2_deg	5.119
r_mcangle_it	3.039
r_mcbond_it	1.746
r_mcbond_other	1.746
r_angle_refined_deg	1.028
r_angle_other_deg	0.346
r_chiral_restr	0.048
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6507
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms	178

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.