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

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
2.142

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.542α = 90
b = 90.729β = 109.519
c = 77.678γ = 90
Symmetry
Space GroupP 1 21 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
11.9545.3699.10.0950.1140.0640.9958.73.160013
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)
11.95299.40.5923

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 REPLACEMENTTHROUGHOUT1.9538.59259988289899.0230.1750.17420.1750.20120.2018RANDOM31.492
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]
-0.445-0.5721.905-0.843
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.272
r_dihedral_angle_6_deg15.862
r_dihedral_angle_3_deg13.337
r_dihedral_angle_1_deg9.324
r_lrange_it7.934
r_lrange_other7.894
r_scangle_it5.434
r_scangle_other5.434
r_scbond_it3.567
r_scbond_other3.567
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.272
r_dihedral_angle_6_deg15.862
r_dihedral_angle_3_deg13.337
r_dihedral_angle_1_deg9.324
r_lrange_it7.934
r_lrange_other7.894
r_scangle_it5.434
r_scangle_other5.434
r_scbond_it3.567
r_scbond_other3.567
r_mcangle_other3.063
r_mcangle_it3.059
r_mcbond_it2.242
r_mcbond_other2.016
r_angle_refined_deg1.094
r_angle_other_deg0.401
r_nbd_refined0.202
r_nbd_other0.194
r_symmetry_nbd_other0.192
r_symmetry_nbd_refined0.191
r_nbtor_refined0.178
r_xyhbond_nbd_refined0.156
r_metal_ion_refined0.145
r_symmetry_xyhbond_nbd_refined0.142
r_symmetry_nbtor_other0.082
r_chiral_restr0.056
r_symmetry_xyhbond_nbd_other0.033
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6292
Nucleic Acid Atoms
Solvent Atoms364
Heterogen Atoms272

Software

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