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