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Crystal Structure of Autotaxin (ENPP2) with Type IV Inhibitor
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 2.29 46.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.603 α = 105.724 b = 62.885 β = 96.546 c = 64.594 γ = 93.615
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 43.19 96 0.097 0.137 0.097 0.983 5.5 1.7 52110
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 2.05 94.4 0.588 1.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2 43.19 52102 2571 95.998 0.173 0.1709 0.2175 0.2086 RANDOM 31.226
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] -0.263 0.065 0.689 -0.355 -0.166 0.434
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.526 r_dihedral_angle_2_deg 14.969 r_dihedral_angle_3_deg 14.076 r_lrange_other 12.431 r_lrange_it 12.424 r_scangle_it 11.042 r_scangle_other 11.031 r_dihedral_angle_1_deg 9.823 r_scbond_other 8.568 r_scbond_it 8.567
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.526 r_dihedral_angle_2_deg 14.969 r_dihedral_angle_3_deg 14.076 r_lrange_other 12.431 r_lrange_it 12.424 r_scangle_it 11.042 r_scangle_other 11.031 r_dihedral_angle_1_deg 9.823 r_scbond_other 8.568 r_scbond_it 8.567 r_mcangle_it 6.298 r_mcangle_other 6.297 r_mcbond_it 5.636 r_mcbond_other 5.096 r_angle_refined_deg 1.382 r_angle_other_deg 0.484 r_nbd_other 0.232 r_nbd_refined 0.213 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.166 r_symmetry_nbd_refined 0.165 r_metal_ion_refined 0.14 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_refined 0.082 r_chiral_restr 0.072 r_symmetry_xyhbond_nbd_other 0.028 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6339 Nucleic Acid Atoms Solvent Atoms 368 Heterogen Atoms 229
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing Coot model building MolProbity model building XDS data reduction PDB-REDO refinement