7Z0N

Structure-Based Design of a Novel Class of Autotaxin Inhibitors Based on Endogenous Allosteric Modulators

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	ATX was incubated with each screened compound at a 1:10 (protein:compound) ratio for at least 30 minutes. Crystals were grown for at least 7 days in a 24-well optimization screen: 18 to 20% PEG 3350, 0.1 to 0.4 M NaSCN, and 0.1 to 0.4 M NH4I.

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.788	α = 90
b = 89.607	β = 102.908
c = 77.55	γ = 90

Symmetry
Space Group	P 1 21 1

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	DECTRIS PILATUS 2M-F		2020-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.999995	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2.4	46.13	99.9	0.099	0.136	0.093	0.982	7.8	3.4		32870

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	100		0.621	0.849	0.576	0.76	1.7	3.5

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5XR9	2.4	46.13	32852	1631	99.933	0.201	0.1978	0.263	45.694

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]
-2.47		0.565	3.491		-1.158

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.532
r_dihedral_angle_4_deg	17.435
r_dihedral_angle_3_deg	15.258
r_dihedral_angle_1_deg	7.247
r_lrange_it	4.806
r_lrange_other	4.789
r_scangle_it	2.744
r_scangle_other	2.744
r_mcangle_it	2.611
r_mcangle_other	2.611
r_scbond_it	1.806
r_scbond_other	1.806
r_mcbond_it	1.716
r_mcbond_other	1.707
r_angle_refined_deg	1.484
r_angle_other_deg	1.227
r_symmetry_nbd_refined	0.237
r_nbd_other	0.234
r_metal_ion_refined	0.226
r_nbd_refined	0.203
r_symmetry_nbd_other	0.198
r_symmetry_xyhbond_nbd_refined	0.19
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.169
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.063
r_symmetry_xyhbond_nbd_other	0.009
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6381
Nucleic Acid Atoms
Solvent Atoms	271
Heterogen Atoms	194

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
Coot	model building
MolProbity	model building
PHASER	phasing