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Crystal Structure of rat Autotaxin in complex with 3-[5-cyclopropyl-6-(oxan-4-yloxy)pyridin-3-yl]-4-methyl-1H-1,2,4-triazol-5-one
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model in house model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 15.3 mg/mL protein in 20mM BICINE/NaOH pH8.5, 150mM NaCl, 0.02% NaN3 mixed 50-70% with 50-30% reservoir consisting of 11-17% PEG3350, 0.1M Na-acetate pH4.5, 0.2M Ca-acetate, total volume 200nL
Crystal Properties Matthews coefficient Solvent content 2.37 48.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.281 α = 90 b = 91.405 β = 90 c = 119.929 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 PSI PILATUS 6M 2014-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000070 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.81 43.09 99.9 0.107 0.116 0.999 12.1 6.662 84989 37.048
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.81 1.86 99.8 2.256 2.439 0.336 0.89 6.846
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 inhouse model 1.81 43.09 77110 4012 95.43 0.1949 0.1929 0.193 0.233 0.2329 RANDOM 37.006
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] 0.23 -0.33 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.27 r_dihedral_angle_4_deg 15.274 r_dihedral_angle_3_deg 14.246 r_dihedral_angle_1_deg 6.424 r_mcangle_it 3.546 r_scbond_it 3.506 r_mcbond_it 2.455 r_angle_refined_deg 1.567 r_chiral_restr 0.109 r_bond_refined_d 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.27 r_dihedral_angle_4_deg 15.274 r_dihedral_angle_3_deg 14.246 r_dihedral_angle_1_deg 6.424 r_mcangle_it 3.546 r_scbond_it 3.506 r_mcbond_it 2.455 r_angle_refined_deg 1.567 r_chiral_restr 0.109 r_bond_refined_d 0.013 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6500 Nucleic Acid Atoms Solvent Atoms 404 Heterogen Atoms 126
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing