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Crystal Structure of rat Autotaxin in complex with 2-[6-(4-acetylpiperazin-1-yl)-2,4-dioxo-1H-quinazolin-3-yl]-N-[(3,4-dichlorophenyl)methyl]acetamide
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 2.39 48.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.102 α = 90 b = 91.847 β = 90 c = 120.483 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 2014-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000050 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 2.05 45.92 99.9 0.185 0.201 0.995 8.19 6.662 59223 36.689
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 2.05 2.1 99.8 1.725 1.874 0.394 1.11 6.594
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 2.05 45.92 53746 2867 95.6 0.203 0.2005 0.2009 0.2503 0.2507 RANDOM 32.724
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] -1.21 0.8 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.34 r_dihedral_angle_4_deg 17.625 r_dihedral_angle_3_deg 14.383 r_dihedral_angle_1_deg 6.377 r_mcangle_it 3.305 r_scbond_it 2.934 r_mcbond_it 2.08 r_angle_refined_deg 1.556 r_chiral_restr 0.104 r_bond_refined_d 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.34 r_dihedral_angle_4_deg 17.625 r_dihedral_angle_3_deg 14.383 r_dihedral_angle_1_deg 6.377 r_mcangle_it 3.305 r_scbond_it 2.934 r_mcbond_it 2.08 r_angle_refined_deg 1.556 r_chiral_restr 0.104 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6500 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 138
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing