9FTN | pdb_00009ftn

Crystal Structure of Autotaxin (ENPP2) with Type VI Inhibitor, a Novel Class of Inhibitors with Three-Point Lock Binding Mode

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
2.21	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.935	α = 98.991
b = 63.558	β = 105.207
c = 70.599	γ = 99.647

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	2.9	47.78	96.8	0.13	0.184	0.13	0.965	3.1	1.7		18732

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	2.9	3.08	96.9		0.603		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	2.9	44.166	18730	964	96.846	0.21	0.2066	0.2113	0.2681	0.2716	RANDOM	52.241

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]
-5.382	4.93	-0.435	-0.862	2.522	2.759

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.151
r_dihedral_angle_3_deg	12.367
r_dihedral_angle_6_deg	11.731
r_dihedral_angle_1_deg	6.7
r_lrange_it	4.741
r_lrange_other	4.728
r_mcangle_it	1.752
r_mcangle_other	1.752
r_scangle_it	1.57
r_scangle_other	1.57
r_mcbond_it	0.993
r_mcbond_other	0.983
r_scbond_it	0.943
r_scbond_other	0.943
r_angle_refined_deg	0.865
r_angle_other_deg	0.333
r_nbd_other	0.201
r_nbd_refined	0.175
r_symmetry_nbd_other	0.174
r_nbtor_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.146
r_symmetry_nbd_refined	0.144
r_metal_ion_refined	0.126
r_xyhbond_nbd_refined	0.115
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.042
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6287
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	137

Software

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