7G7G | pdb_00007g7g

Crystal Structure of rat Autotaxin in complex with 2-[7-(1-acetylpiperidin-4-yl)-4-oxopyrido[1,2-a]pyrimidin-3-yl]-N-[(3,4-dichlorophenyl)methyl]-N-methylacetamide, i.e. SMILES c1(ccc(c(c1)Cl)Cl)CN(C(=O)CC1=CN=C2C=CC(=CN2C1=O)C1CCN(CC1)C(=O)C)C with IC50=0.798931 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
2.35	47.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.756	α = 90
b = 91.705	β = 90
c = 119.371	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		2015-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.999920	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	1.4	48.61	99.9	0.055	0.06	0.999	15.7	6.589		180620			27.634

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	1.4	1.44	99.9		2.046	2.222	0.371	0.89	6.559

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	1.4	48.61	164553	8698	95.91	0.1874	0.1862	0.1859	0.2094	0.2092	RANDOM	26.878

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]
-0.69			0.12		0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.209
r_dihedral_angle_4_deg	14.544
r_dihedral_angle_1_deg	13.098
r_dihedral_angle_3_deg	12.823
r_mcangle_it	3.17
r_scbond_it	3.162
r_mcbond_it	2.137
r_angle_refined_deg	1.883
r_chiral_restr	0.131
r_bond_refined_d	0.017

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.209
r_dihedral_angle_4_deg	14.544
r_dihedral_angle_1_deg	13.098
r_dihedral_angle_3_deg	12.823
r_mcangle_it	3.17
r_scbond_it	3.162
r_mcbond_it	2.137
r_angle_refined_deg	1.883
r_chiral_restr	0.131
r_bond_refined_d	0.017
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6500
Nucleic Acid Atoms
Solvent Atoms	656
Heterogen Atoms	147

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.