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Crystal Structure of rat Autotaxin in complex with N-(5-chloro-2,3-dihydro-1H-inden-2-yl)-6-(oxetan-3-ylsulfonyl)-5,7-dihydropyrrolo[3,4-d]pyrimidin-2-amine, i.e. SMILES Clc1cc2c(cc1)C[C@@H](C2)Nc1ncc2CN(Cc2n1)S(=O)(=O)C1COC1 with IC50=0.0214337 microM
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 47.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.577 α = 90 b = 91.265 β = 90 c = 119.204 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 2018-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000000 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.62 72.47 99.9 0.13 9.65 6.645 116219 29.63
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.62 1.66 100 2.353 0.77 6.77
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 1.62 72.47 88905 4649 80.7 0.168 0.166 0.207 0.1943 RANDOM 22.81
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] 0.06 0.02 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.587 r_dihedral_angle_1_deg 24.484 r_dihedral_angle_4_deg 16.172 r_dihedral_angle_3_deg 12.879 r_mcangle_it 3.778 r_mcbond_it 2.606 r_mcbond_other 2.589 r_angle_refined_deg 1.937 r_angle_other_deg 1.481 r_chiral_restr 0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.587 r_dihedral_angle_1_deg 24.484 r_dihedral_angle_4_deg 16.172 r_dihedral_angle_3_deg 12.879 r_mcangle_it 3.778 r_mcbond_it 2.606 r_mcbond_other 2.589 r_angle_refined_deg 1.937 r_angle_other_deg 1.481 r_chiral_restr 0.105 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6500 Nucleic Acid Atoms Solvent Atoms 658 Heterogen Atoms 173
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing