7G6Y | pdb_00007g6y

Crystal Structure of rat Autotaxin in complex with 1-[4-[[7-[(3,4-difluorophenyl)methyl]-9-methyl-8-oxopurin-2-yl]amino]benzoyl]piperidine-4-sulfonamide, i.e. SMILES c1nc(nc2c1N(C(=O)N2C)Cc1ccc(c(c1)F)F)Nc1ccc(cc1)C(=O)N1CCC(CC1)S(=O)(=O)N with IC50=0.00233021 microM

X-RAY DIFFRACTION

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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	48.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.007	α = 90
b = 92.008	β = 90
c = 120.287	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		2014-05-10	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	1.48	48.9	98.8	0.085	0.092	0.999	12.59	6.705		153568			26.802

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	1.48	1.52	97.7		2.001	2.159	0.375	0.95	6.975

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	1.48	48.9	140266	7569	95.2	0.1831	0.1817	0.1813	0.2091	0.2089	RANDOM	24.828

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]
-0.44			-0.18		0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.232
r_dihedral_angle_4_deg	15.442
r_dihedral_angle_3_deg	13.159
r_dihedral_angle_1_deg	6.317
r_scbond_it	3.104
r_mcangle_it	2.975
r_mcbond_it	1.993
r_angle_refined_deg	1.866
r_chiral_restr	0.132
r_bond_refined_d	0.017
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6500
Nucleic Acid Atoms
Solvent Atoms	677
Heterogen Atoms	142

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing