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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, HANGING DROP 293 PEG3350, NaSCN and NH4I
Crystal Properties Matthews coefficient Solvent content 2.2 43.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.927 α = 90 b = 88.012 β = 103.1 c = 77.356 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 2016-05-29 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 2.4 75.34 98.3 41.9 4.5 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 2.4 75.34 30558 1568 99.71 0.22713 0.22493 0.2252 0.26966 0.2662 RANDOM 59.659
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] -0.58 1.57 -3.34 2.88
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 82.075 r_sphericity_free 38.132 r_dihedral_angle_2_deg 33.536 r_dihedral_angle_4_deg 16.647 r_dihedral_angle_3_deg 14.131 r_dihedral_angle_1_deg 7.009 r_long_range_B_refined 3.597 r_long_range_B_other 3.597 r_angle_refined_deg 1.377 r_angle_other_deg 0.934
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 82.075 r_sphericity_free 38.132 r_dihedral_angle_2_deg 33.536 r_dihedral_angle_4_deg 16.647 r_dihedral_angle_3_deg 14.131 r_dihedral_angle_1_deg 7.009 r_long_range_B_refined 3.597 r_long_range_B_other 3.597 r_angle_refined_deg 1.377 r_angle_other_deg 0.934 r_mcangle_it 0.608 r_mcangle_other 0.608 r_scangle_other 0.388 r_mcbond_it 0.323 r_mcbond_other 0.32 r_scbond_it 0.217 r_scbond_other 0.215 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6251 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 181
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing