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Exploiting an Asp-Glu switch in Glycogen Synthase Kinase 3 to design paralog selective inhibitors for use in acute myeloid leukemia
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PTE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 20% PEG MME 5,000 and 0.1 M Bis-Tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.76 55.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.957 α = 90 b = 84.223 β = 94.69 c = 117.218 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD MARMOSAIC 225 mm CCD 2016-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97875 APS 21-ID-F
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 2.85 50 99 13.3 3.8 24568
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 2.85 2.95 0.66 1.8 3.8
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 4PTE 2.85 47.41 22658 1206 97.02 0.19962 0.196 0.1984 0.26797 0.2625 RANDOM 79.21
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] 0.02 0.05 -0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.676 r_dihedral_angle_3_deg 17.215 r_dihedral_angle_4_deg 16.321 r_long_range_B_refined 10.574 r_long_range_B_other 10.573 r_mcangle_other 8.508 r_mcangle_it 8.507 r_scangle_other 7.995 r_dihedral_angle_1_deg 7.5 r_mcbond_it 5.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.676 r_dihedral_angle_3_deg 17.215 r_dihedral_angle_4_deg 16.321 r_long_range_B_refined 10.574 r_long_range_B_other 10.573 r_mcangle_other 8.508 r_mcangle_it 8.507 r_scangle_other 7.995 r_dihedral_angle_1_deg 7.5 r_mcbond_it 5.71 r_mcbond_other 5.699 r_scbond_it 5.358 r_scbond_other 5.357 r_angle_refined_deg 1.709 r_angle_other_deg 1.027 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.003 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 5155 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing