9FXU | pdb_00009fxu

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XR9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293ATX 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 coefficientSolvent content
2.448.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.706α = 99.553
b = 63.424β = 105.153
c = 70.306γ = 99.268
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2021-05-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.965459ESRFMASSIF-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.2547.5997.90.0910.1140.0680.9787.32.740044
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.3297.30.4772.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.2547.5940041202597.8640.1790.17720.18190.21020.2146RANDOM53.694
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]
-0.2450.8361.627-0.1280.046-0.736
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.451
r_dihedral_angle_6_deg15.297
r_dihedral_angle_3_deg13.576
r_dihedral_angle_1_deg10.551
r_lrange_it8.233
r_lrange_other8.206
r_scangle_it4.485
r_scangle_other4.29
r_mcangle_other3.235
r_mcangle_it3.234
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.451
r_dihedral_angle_6_deg15.297
r_dihedral_angle_3_deg13.576
r_dihedral_angle_1_deg10.551
r_lrange_it8.233
r_lrange_other8.206
r_scangle_it4.485
r_scangle_other4.29
r_mcangle_other3.235
r_mcangle_it3.234
r_scbond_it2.8
r_scbond_other2.68
r_mcbond_it2.298
r_mcbond_other2.024
r_angle_refined_deg1.212
r_angle_other_deg0.422
r_nbd_other0.222
r_nbd_refined0.208
r_symmetry_nbd_other0.192
r_nbtor_refined0.182
r_metal_ion_refined0.163
r_symmetry_xyhbond_nbd_refined0.162
r_xyhbond_nbd_refined0.156
r_symmetry_nbd_refined0.15
r_symmetry_nbtor_other0.084
r_symmetry_xyhbond_nbd_other0.069
r_chiral_restr0.059
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6305
Nucleic Acid Atoms
Solvent Atoms255
Heterogen Atoms192

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing
Cootmodel building
MolProbitymodel building
XDSdata reduction
PDB-REDOrefinement