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Structure-Based Design of a Novel Class of Autotaxin Inhibitors Based on Endogenous Allosteric Modulators
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XR9
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 2.34 47.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.788 α = 90 b = 89.607 β = 102.908 c = 77.55 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 PILATUS 2M-F 2020-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.999995 SLS X06DA
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 2.4 46.13 99.9 0.099 0.136 0.093 0.982 7.8 3.4 32870
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 100 0.621 0.849 0.576 0.76 1.7 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5XR9 2.4 46.13 32852 1631 99.933 0.201 0.1978 0.2017 0.263 0.2721 45.694
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] -2.47 0.565 3.491 -1.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.532 r_dihedral_angle_4_deg 17.435 r_dihedral_angle_3_deg 15.258 r_dihedral_angle_1_deg 7.247 r_lrange_it 4.806 r_lrange_other 4.789 r_scangle_it 2.744 r_scangle_other 2.744 r_mcangle_it 2.611 r_mcangle_other 2.611
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.532 r_dihedral_angle_4_deg 17.435 r_dihedral_angle_3_deg 15.258 r_dihedral_angle_1_deg 7.247 r_lrange_it 4.806 r_lrange_other 4.789 r_scangle_it 2.744 r_scangle_other 2.744 r_mcangle_it 2.611 r_mcangle_other 2.611 r_scbond_it 1.806 r_scbond_other 1.806 r_mcbond_it 1.716 r_mcbond_other 1.707 r_angle_refined_deg 1.484 r_angle_other_deg 1.227 r_symmetry_nbd_refined 0.237 r_nbd_other 0.234 r_metal_ion_refined 0.226 r_nbd_refined 0.203 r_symmetry_nbd_other 0.198 r_symmetry_xyhbond_nbd_refined 0.19 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.169 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.063 r_symmetry_xyhbond_nbd_other 0.009 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6381 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 194
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling Coot model building MolProbity model building PHASER phasing