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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 2.21 44.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.826 α = 90 b = 88.857 β = 103.08 c = 77.293 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 PILATUS 2M 2016-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.9801 SLS X06DA
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 75.29 97.1 32.6 3.8 50000
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 2XR9 2.1 75.29 45218 2344 98.35 0.24018 0.23789 0.2434 0.28607 0.2892 RANDOM 47.435
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] -0.81 0.37 -1.51 1.93
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 77.525 r_dihedral_angle_2_deg 32.842 r_dihedral_angle_4_deg 15.905 r_dihedral_angle_3_deg 12.618 r_dihedral_angle_1_deg 6.613 r_long_range_B_refined 5.372 r_long_range_B_other 5.372 r_angle_refined_deg 1.249 r_angle_other_deg 0.975 r_mcangle_it 0.462
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 77.525 r_dihedral_angle_2_deg 32.842 r_dihedral_angle_4_deg 15.905 r_dihedral_angle_3_deg 12.618 r_dihedral_angle_1_deg 6.613 r_long_range_B_refined 5.372 r_long_range_B_other 5.372 r_angle_refined_deg 1.249 r_angle_other_deg 0.975 r_mcangle_it 0.462 r_mcangle_other 0.462 r_scangle_other 0.307 r_mcbond_it 0.247 r_mcbond_other 0.244 r_scbond_it 0.198 r_scbond_other 0.198 r_chiral_restr 0.085 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6268 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 228
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing