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Structure-based evolution of a hybrid steroid series of Autotaxin inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XR9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG3350, NaSCN and NH4I
Crystal Properties Matthews coefficient Solvent content 2.22 44.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.995 α = 90 b = 89.173 β = 103.12 c = 77.289 γ = 90
Symmetry Space Group P 1 21 1
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 DECTRIS EIGER X 16M 2016-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 75.27 89.2 19.1 27 45214
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 2XR9 2.1 75.27 45214 2343 97.91 0.20338 0.20107 0.24909 0.2383 RANDOM 37.019
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] -2.91 -0.18 2.21 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.452 r_dihedral_angle_4_deg 16.566 r_dihedral_angle_3_deg 13.23 r_dihedral_angle_1_deg 6.718 r_long_range_B_refined 4.14 r_long_range_B_other 4.14 r_angle_refined_deg 1.515 r_mcangle_it 1.388 r_mcangle_other 1.388 r_scangle_other 1.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.452 r_dihedral_angle_4_deg 16.566 r_dihedral_angle_3_deg 13.23 r_dihedral_angle_1_deg 6.718 r_long_range_B_refined 4.14 r_long_range_B_other 4.14 r_angle_refined_deg 1.515 r_mcangle_it 1.388 r_mcangle_other 1.388 r_scangle_other 1.338 r_angle_other_deg 0.964 r_scbond_it 0.795 r_scbond_other 0.795 r_mcbond_it 0.791 r_mcbond_other 0.772 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6242 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 268
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing