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

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
2.2144

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.935α = 98.991
b = 63.558β = 105.207
c = 70.599γ = 99.647
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
12.947.7896.80.130.1840.130.9653.11.718732
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)
12.93.0896.90.6031.7

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 REPLACEMENTTHROUGHOUT2.944.1661873096496.8460.210.20660.21130.26810.2716RANDOM52.241
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]
-5.3824.93-0.435-0.8622.5222.759
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.151
r_dihedral_angle_3_deg12.367
r_dihedral_angle_6_deg11.731
r_dihedral_angle_1_deg6.7
r_lrange_it4.741
r_lrange_other4.728
r_mcangle_it1.752
r_mcangle_other1.752
r_scangle_it1.57
r_scangle_other1.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.151
r_dihedral_angle_3_deg12.367
r_dihedral_angle_6_deg11.731
r_dihedral_angle_1_deg6.7
r_lrange_it4.741
r_lrange_other4.728
r_mcangle_it1.752
r_mcangle_other1.752
r_scangle_it1.57
r_scangle_other1.57
r_mcbond_it0.993
r_mcbond_other0.983
r_scbond_it0.943
r_scbond_other0.943
r_angle_refined_deg0.865
r_angle_other_deg0.333
r_nbd_other0.201
r_nbd_refined0.175
r_symmetry_nbd_other0.174
r_nbtor_refined0.17
r_symmetry_xyhbond_nbd_refined0.146
r_symmetry_nbd_refined0.144
r_metal_ion_refined0.126
r_xyhbond_nbd_refined0.115
r_symmetry_nbtor_other0.088
r_chiral_restr0.042
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6287
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms137

Software

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