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Crystal structure of Autotaxin (ENPP2) with tauroursodeoxycholic acid (TUDCA) and lysophosphatidic acid (LPA)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% PEG 3350, 0.3M sodium thiocyanate, 0.2M sodium iodide, 350 uM TUDCA, 100 uM LPA
Crystal Properties Matthews coefficient Solvent content 2.32 46.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.197 α = 90 b = 93.051 β = 90 c = 149.68 γ = 90
Symmetry Space Group P 21 21 21
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 6M-F 2015-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97626 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 46.53 99.8 0.165 0.074 0.995 8.6 5.9 82325
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 99.3 2.551 1.14 0.259 1 5.8 4435
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 (Observed) 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 1.8 79.03 78197 4048 99.66 0.1893 0.1879 0.1961 0.2163 0.2237 RANDOM 32.905
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] -0.22 0.58 -0.36
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 54.574 r_sphericity_bonded 50.99 r_dihedral_angle_2_deg 34.002 r_dihedral_angle_4_deg 17.274 r_dihedral_angle_3_deg 11.542 r_dihedral_angle_1_deg 6.424 r_mcangle_it 2.945 r_mcbond_it 1.924 r_mcbond_other 1.924 r_angle_refined_deg 1.466
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 54.574 r_sphericity_bonded 50.99 r_dihedral_angle_2_deg 34.002 r_dihedral_angle_4_deg 17.274 r_dihedral_angle_3_deg 11.542 r_dihedral_angle_1_deg 6.424 r_mcangle_it 2.945 r_mcbond_it 1.924 r_mcbond_other 1.924 r_angle_refined_deg 1.466 r_angle_other_deg 1.112 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6302 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 182
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction Coot model building