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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 PEG 3350, NaSCN and NH4I
Crystal Properties Matthews coefficient Solvent content 2.13 42.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.618 α = 103.43 b = 61.729 β = 98.18 c = 63.696 γ = 93.5
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 2015-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00000 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 1.95 61.15 98.8 18.9 3.9 53155
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 1.95 61.15 53155 2761 97.96 0.18309 0.18102 0.1873 0.22295 0.2302 RANDOM 28.509
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] -0.74 -0.11 -0.55 0.62 0.61 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.621 r_dihedral_angle_4_deg 18.923 r_dihedral_angle_3_deg 14.276 r_dihedral_angle_1_deg 6.706 r_long_range_B_refined 4.179 r_long_range_B_other 4.179 r_scangle_other 2.139 r_mcangle_it 1.787 r_mcangle_other 1.787 r_angle_refined_deg 1.631
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.621 r_dihedral_angle_4_deg 18.923 r_dihedral_angle_3_deg 14.276 r_dihedral_angle_1_deg 6.706 r_long_range_B_refined 4.179 r_long_range_B_other 4.179 r_scangle_other 2.139 r_mcangle_it 1.787 r_mcangle_other 1.787 r_angle_refined_deg 1.631 r_scbond_it 1.307 r_scbond_other 1.307 r_mcbond_it 1.063 r_mcbond_other 1.046 r_angle_other_deg 0.98 r_chiral_restr 0.09 r_bond_refined_d 0.012 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 6238 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 200
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing