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Crystal structure of Autotaxin (ENPP2) with tauroursodeoxycholic acid (TUDCA)
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 20% PEG 3350, 0.3M sodium thiocyanate, 0.2 ammonium iodide, 350 uM TUDCA
Crystal Properties Matthews coefficient Solvent content 2.27 45.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.88 α = 83.84 b = 77.832 β = 79.29 c = 92.437 γ = 77.08
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 2014-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87257 ESRF ID23-2
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 2 46.79 97.9 0.177 0.109 0.988 5.6 3.6 110991
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 2 2.03 92 1.613 0.987 0.336 0.8 3.5 5181
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 (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 2xr9 2 90.61 103276 5310 95.81 0.1949 0.1933 0.1998 0.2267 0.2317 RANDOM 35.513
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] -0.08 -0.59 0.13 0.44 -0.18 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.377 r_sphericity_bonded 31.474 r_sphericity_free 29.763 r_dihedral_angle_4_deg 15.05 r_dihedral_angle_3_deg 12.469 r_dihedral_angle_1_deg 6.482 r_mcangle_it 2.909 r_mcbond_it 1.83 r_mcbond_other 1.824 r_angle_refined_deg 1.435
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.377 r_sphericity_bonded 31.474 r_sphericity_free 29.763 r_dihedral_angle_4_deg 15.05 r_dihedral_angle_3_deg 12.469 r_dihedral_angle_1_deg 6.482 r_mcangle_it 2.909 r_mcbond_it 1.83 r_mcbond_other 1.824 r_angle_refined_deg 1.435 r_angle_other_deg 0.982 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12602 Nucleic Acid Atoms Solvent Atoms 589 Heterogen Atoms 517
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction Coot model building PHASER phasing