7G2Q | pdb_00007g2q

Crystal Structure of rat Autotaxin in complex with 1-[2-[2-cyclopropyl-6-(oxan-4-ylmethoxy)pyridine-4-carbonyl]-1,3,4,6-tetrahydropyrrolo[3,4-c]pyrrole-5-carbonyl]piperidine-4-sulfonamide, i.e. SMILES N1(C(=O)N2CC3=C(CN(C3)C(=O)c3cc(nc(c3)C3CC3)OCC3CCOCC3)C2)CC[C@@H](CC1)S(=O)(=O)N with IC50=0.00248328 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
2.39	48.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.089	α = 90
b = 91.991	β = 90
c = 120.355	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		2016-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.999890	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	1.83	42.96	96	0.119	0.13	0.998	10.55	6.5		79696			35.561

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	1.83	1.88	99.7		2.267	2.458	0.323	0.77	6.701

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	1.83	43.2	66438	3456	84.32	0.1993	0.1971	0.2056	0.2414	0.2451	RANDOM	33.367

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]
-1.07			0.35		0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.156
r_dihedral_angle_4_deg	14.545
r_dihedral_angle_3_deg	13.052
r_dihedral_angle_1_deg	11.781
r_mcangle_it	3.248
r_mcbond_other	2.123
r_mcbond_it	2.122
r_angle_refined_deg	1.605
r_angle_other_deg	0.995
r_chiral_restr	0.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.156
r_dihedral_angle_4_deg	14.545
r_dihedral_angle_3_deg	13.052
r_dihedral_angle_1_deg	11.781
r_mcangle_it	3.248
r_mcbond_other	2.123
r_mcbond_it	2.122
r_angle_refined_deg	1.605
r_angle_other_deg	0.995
r_chiral_restr	0.095
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6500
Nucleic Acid Atoms
Solvent Atoms	451
Heterogen Atoms	143

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.