7G79 | pdb_00007g79

Crystal Structure of rat Autotaxin in complex with 1-[(3aS,6aS)-5-[2-cyclopropyl-6-(oxan-4-ylmethoxy)pyridine-4-carbonyl]-1,3,3a,4,6,6a-hexahydropyrrolo[3,4-c]pyrrol-2-yl]-3-(1H-triazol-5-yl)propan-1-one, i.e. SMILES N1(C(=O)c2cc(nc(c2)C2CC2)OCC2CCOCC2)C[C@H]2[C@H](C1)CN(C2)C(=O)CCC1=CN=NN1 with IC50=0.250768 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	48.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.245	α = 90
b = 91.757	β = 90
c = 119.644	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		2014-10-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000010	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	1.72	48.78	99.9	0.112	0.122	0.998	11.78	6.662		98984			32.305

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	1.72	1.76	99.9		1.875	2.034	0.407	1.18	6.733

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	1.72	48.78	90423	4736	96.16	0.1856	0.1841	0.1839	0.214	0.2144	RANDOM	31.165

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]
-0.2			-0.02		0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.395
r_dihedral_angle_4_deg	15.292
r_dihedral_angle_3_deg	13.267
r_dihedral_angle_1_deg	6.413
r_scbond_it	3.285
r_mcangle_it	3.243
r_mcbond_it	2.21
r_angle_refined_deg	1.631
r_chiral_restr	0.113
r_bond_refined_d	0.014

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.395
r_dihedral_angle_4_deg	15.292
r_dihedral_angle_3_deg	13.267
r_dihedral_angle_1_deg	6.413
r_scbond_it	3.285
r_mcangle_it	3.243
r_mcbond_it	2.21
r_angle_refined_deg	1.631
r_chiral_restr	0.113
r_bond_refined_d	0.014
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6500
Nucleic Acid Atoms
Solvent Atoms	535
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.