9FXY | pdb_00009fxy

Crystal Structure of Autotaxin (ENPP2) with Type IV Inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XR9

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
2.29	46.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.603	α = 105.724
b = 62.885	β = 96.546
c = 64.594	γ = 93.615

Symmetry
Space Group	P 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 PILATUS3 2M		2021-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.965459	ESRF	MASSIF-1

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	43.19	96	0.097	0.137	0.097	0.983	5.5	1.7		52110

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05	94.4		0.588		1.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	2	43.19	52102	2571	95.998	0.173	0.1709	0.1743	0.2175	0.221	RANDOM	31.226

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]
-0.263	0.065	0.689	-0.355	-0.166	0.434

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.526
r_dihedral_angle_2_deg	14.969
r_dihedral_angle_3_deg	14.076
r_lrange_other	12.431
r_lrange_it	12.424
r_scangle_it	11.042
r_scangle_other	11.031
r_dihedral_angle_1_deg	9.823
r_scbond_other	8.568
r_scbond_it	8.567
r_mcangle_it	6.298
r_mcangle_other	6.297
r_mcbond_it	5.636
r_mcbond_other	5.096
r_angle_refined_deg	1.382
r_angle_other_deg	0.484
r_nbd_other	0.232
r_nbd_refined	0.213
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.166
r_symmetry_nbd_refined	0.165
r_metal_ion_refined	0.14
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_refined	0.082
r_chiral_restr	0.072
r_symmetry_xyhbond_nbd_other	0.028
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6339
Nucleic Acid Atoms
Solvent Atoms	368
Heterogen Atoms	229

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing
Coot	model building
MolProbity	model building
XDS	data reduction
PDB-REDO	refinement