9FXW | pdb_00009fxw

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
2.1	42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.542	α = 90
b = 90.729	β = 109.519
c = 77.678	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 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	1.95	45.36	99.1	0.095	0.114	0.064	0.995	8.7	3.1		60013

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	1.95	2	99.4		0.592		3

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	1.95	38.592	59988	2898	99.023	0.175	0.1742	0.175	0.2012	0.2018	RANDOM	31.492

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]
-0.445		-0.572	1.905		-0.843

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.272
r_dihedral_angle_6_deg	15.862
r_dihedral_angle_3_deg	13.337
r_dihedral_angle_1_deg	9.324
r_lrange_it	7.934
r_lrange_other	7.894
r_scangle_it	5.434
r_scangle_other	5.434
r_scbond_it	3.567
r_scbond_other	3.567
r_mcangle_other	3.063
r_mcangle_it	3.059
r_mcbond_it	2.242
r_mcbond_other	2.016
r_angle_refined_deg	1.094
r_angle_other_deg	0.401
r_nbd_refined	0.202
r_nbd_other	0.194
r_symmetry_nbd_other	0.192
r_symmetry_nbd_refined	0.191
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.156
r_metal_ion_refined	0.145
r_symmetry_xyhbond_nbd_refined	0.142
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.056
r_symmetry_xyhbond_nbd_other	0.033
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6292
Nucleic Acid Atoms
Solvent Atoms	364
Heterogen Atoms	272

Software

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