9FXY | pdb_00009fxy

Crystal Structure of Autotaxin (ENPP2) with Type IV Inhibitor


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
2.2946.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.603α = 105.724
b = 62.885β = 96.546
c = 64.594γ = 93.615
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
1243.19960.0970.1370.0970.9835.51.752110
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)
122.0594.40.5881.7

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 REPLACEMENTTHROUGHOUT243.1952102257195.9980.1730.17090.17430.21750.221RANDOM31.226
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]
-0.2630.0650.689-0.355-0.1660.434
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.526
r_dihedral_angle_2_deg14.969
r_dihedral_angle_3_deg14.076
r_lrange_other12.431
r_lrange_it12.424
r_scangle_it11.042
r_scangle_other11.031
r_dihedral_angle_1_deg9.823
r_scbond_other8.568
r_scbond_it8.567
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.526
r_dihedral_angle_2_deg14.969
r_dihedral_angle_3_deg14.076
r_lrange_other12.431
r_lrange_it12.424
r_scangle_it11.042
r_scangle_other11.031
r_dihedral_angle_1_deg9.823
r_scbond_other8.568
r_scbond_it8.567
r_mcangle_it6.298
r_mcangle_other6.297
r_mcbond_it5.636
r_mcbond_other5.096
r_angle_refined_deg1.382
r_angle_other_deg0.484
r_nbd_other0.232
r_nbd_refined0.213
r_symmetry_nbd_other0.193
r_nbtor_refined0.185
r_xyhbond_nbd_refined0.166
r_symmetry_nbd_refined0.165
r_metal_ion_refined0.14
r_symmetry_nbtor_other0.083
r_symmetry_xyhbond_nbd_refined0.082
r_chiral_restr0.072
r_symmetry_xyhbond_nbd_other0.028
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6339
Nucleic Acid Atoms
Solvent Atoms368
Heterogen Atoms229

Software

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