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Crystal Structure of rat Autotaxin in complex with 3-[(2-tert-butyl-4-chloro-5-methylphenoxy)methyl]-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridine
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 48.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.98 α = 90 b = 91.888 β = 90 c = 119.682 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 2013-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000040 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 1.79 45.94 100 0.141 0.153 0.998 9.68 6.686 87837 32.267
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 1.79 1.84 99.9 2.188 2.383 0.301 0.81 6.372
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT inhouse model 1.79 45.94 79339 4197 95.15 0.1919 0.1898 0.2331 0.1995 RANDOM 29.795
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] -0.2 -0.18 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.782 r_dihedral_angle_4_deg 14.653 r_dihedral_angle_3_deg 13.42 r_dihedral_angle_1_deg 6.427 r_mcangle_it 3.14 r_scbond_it 2.801 r_mcbond_it 2.042 r_angle_refined_deg 1.568 r_chiral_restr 0.108 r_bond_refined_d 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.782 r_dihedral_angle_4_deg 14.653 r_dihedral_angle_3_deg 13.42 r_dihedral_angle_1_deg 6.427 r_mcangle_it 3.14 r_scbond_it 2.801 r_mcbond_it 2.042 r_angle_refined_deg 1.568 r_chiral_restr 0.108 r_bond_refined_d 0.013 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6484 Nucleic Acid Atoms Solvent Atoms 516 Heterogen Atoms 143
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing