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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 2.4 48.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.706 α = 99.553 b = 63.424 β = 105.153 c = 70.306 γ = 99.268
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 2.25 47.59 97.9 0.091 0.114 0.068 0.978 7.3 2.7 40044
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 2.25 2.32 97.3 0.477 2.6
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 2.25 47.59 40041 2025 97.864 0.179 0.1772 0.1819 0.2102 0.2145 RANDOM 53.694
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] -0.245 0.836 1.627 -0.128 0.046 -0.736
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.451 r_dihedral_angle_6_deg 15.297 r_dihedral_angle_3_deg 13.576 r_dihedral_angle_1_deg 10.551 r_lrange_it 8.233 r_lrange_other 8.206 r_scangle_it 4.485 r_scangle_other 4.29 r_mcangle_other 3.235 r_mcangle_it 3.234
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.451 r_dihedral_angle_6_deg 15.297 r_dihedral_angle_3_deg 13.576 r_dihedral_angle_1_deg 10.551 r_lrange_it 8.233 r_lrange_other 8.206 r_scangle_it 4.485 r_scangle_other 4.29 r_mcangle_other 3.235 r_mcangle_it 3.234 r_scbond_it 2.8 r_scbond_other 2.68 r_mcbond_it 2.298 r_mcbond_other 2.024 r_angle_refined_deg 1.212 r_angle_other_deg 0.422 r_nbd_other 0.222 r_nbd_refined 0.208 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.182 r_metal_ion_refined 0.163 r_symmetry_xyhbond_nbd_refined 0.162 r_xyhbond_nbd_refined 0.156 r_symmetry_nbd_refined 0.15 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_other 0.069 r_chiral_restr 0.059 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6305 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 192
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing Coot model building MolProbity model building XDS data reduction PDB-REDO refinement