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Crystal Structure of rat Autotaxin in complex with 4-pyrrolidin-1-yl-3-[(E)-2-[4-(trifluoromethoxy)phenyl]ethenyl]benzamide
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 2.34 47.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.777 α = 90 b = 91.623 β = 90 c = 118.712 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 2013-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.999970 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 1.73 45.81 99.9 0.127 0.138 0.998 11.03 6.592 95833 30.643
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 1.73 1.77 100 1.859 2.014 0.416 1.13 6.75
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 1.73 45.81 87473 4514 95.98 0.1866 0.185 0.1848 0.2174 0.2175 RANDOM 27.13
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] -0.32 -0.07 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.92 r_dihedral_angle_4_deg 14.879 r_dihedral_angle_3_deg 13.403 r_dihedral_angle_1_deg 6.29 r_mcangle_it 2.834 r_scbond_it 2.667 r_mcbond_it 1.801 r_angle_refined_deg 1.515 r_chiral_restr 0.104 r_bond_refined_d 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.92 r_dihedral_angle_4_deg 14.879 r_dihedral_angle_3_deg 13.403 r_dihedral_angle_1_deg 6.29 r_mcangle_it 2.834 r_scbond_it 2.667 r_mcbond_it 1.801 r_angle_refined_deg 1.515 r_chiral_restr 0.104 r_bond_refined_d 0.012 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6491 Nucleic Acid Atoms Solvent Atoms 495 Heterogen Atoms 152
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing