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Autotaxin in complex with orthosteric site-binder CpdA
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 2.24 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.662 α = 104.159 b = 62.53 β = 98.572 c = 63.638 γ = 93.153
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 43.68 98 0.137 0.194 0.137 0.985 5.6 3.2 52303
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 2.05 96.9 0.798 1.129 0.798 0.437 3.1
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2xr9 2 43.68 52301 2646 97.999 0.204 0.202 0.2422 0.2275 26.899
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] 1.415 1.245 1.265 -1.99 -1.242 0.588
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.592 r_dihedral_angle_4_deg 16.136 r_dihedral_angle_3_deg 12.76 r_dihedral_angle_1_deg 6.853 r_lrange_it 6.454 r_lrange_other 6.386 r_angle_refined_deg 1.218 r_angle_other_deg 1.084 r_mcangle_it 0.728 r_mcangle_other 0.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.592 r_dihedral_angle_4_deg 16.136 r_dihedral_angle_3_deg 12.76 r_dihedral_angle_1_deg 6.853 r_lrange_it 6.454 r_lrange_other 6.386 r_angle_refined_deg 1.218 r_angle_other_deg 1.084 r_mcangle_it 0.728 r_mcangle_other 0.727 r_scangle_it 0.503 r_scangle_other 0.503 r_mcbond_it 0.394 r_mcbond_other 0.389 r_scbond_it 0.362 r_scbond_other 0.362 r_nbd_refined 0.179 r_symmetry_nbd_other 0.17 r_nbd_other 0.168 r_nbtor_refined 0.159 r_symmetry_nbd_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.153 r_xyhbond_nbd_refined 0.111 r_metal_ion_refined 0.095 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.046 r_symmetry_xyhbond_nbd_other 0.019 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6391 Nucleic Acid Atoms Solvent Atoms 527 Heterogen Atoms 199
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling Coot model building PHASER phasing MolProbity model building