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Autotaxin in complex with hybrid compound ziritaxestat (GLPG1690)
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 2.31 46.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.842 α = 90 b = 88.709 β = 102.835 c = 77.03 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 45.92 99.8 0.081 0.111 0.076 0.996 8.2 3.4 32271
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 99.5 0.752 1.032 0.703 0.766 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 2xr9 2.4 45.92 32252 1591 99.731 0.242 0.2413 0.2462 0.2546 0.2591 66.2
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] -0.463 1.187 -0.921 0.764
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.807 r_dihedral_angle_4_deg 13.448 r_dihedral_angle_3_deg 12.345 r_dihedral_angle_1_deg 5.544 r_lrange_it 4.479 r_lrange_other 4.469 r_angle_refined_deg 1.199 r_angle_other_deg 0.997 r_mcangle_it 0.562 r_mcangle_other 0.562
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.807 r_dihedral_angle_4_deg 13.448 r_dihedral_angle_3_deg 12.345 r_dihedral_angle_1_deg 5.544 r_lrange_it 4.479 r_lrange_other 4.469 r_angle_refined_deg 1.199 r_angle_other_deg 0.997 r_mcangle_it 0.562 r_mcangle_other 0.562 r_scangle_it 0.308 r_scangle_other 0.308 r_mcbond_it 0.299 r_mcbond_other 0.298 r_symmetry_nbd_refined 0.258 r_symmetry_xyhbond_nbd_refined 0.217 r_scbond_it 0.196 r_scbond_other 0.194 r_nbtor_refined 0.155 r_nbd_refined 0.148 r_symmetry_nbd_other 0.148 r_nbd_other 0.132 r_xyhbond_nbd_refined 0.096 r_symmetry_nbtor_other 0.077 r_metal_ion_refined 0.074 r_chiral_restr 0.032 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6348 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 224
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling Coot model building PHASER phasing MolProbity model building