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Glycogen synthase kinase-3 beta (GSK3) complex with a covalent [1,2,4]triazolo[1,5-a][1,3,5]triazine inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q5K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 GSK3beta(35-386) aliquots were concentrated to 4.4 mg/ml and used for crystallization trials. GSK3b-inhibitor co-crystals were grown using the sitting drop vapor diffusion technique in 0.2M DL-Malic acid pH 7.0, 20% PEG 3350 as reservoir solution. The protein was previously incubated with 3x molar excess of compound for 3h at 4C. Crystallization drops were prepared from 0.5ul of protein solution and 0.5ul of reservoir, and incubated for 10 days at 20C. Crystals were cryoprotected in 30% Glycerol and frozen in liquid nitrogen prior to data collection.
Crystal Properties Matthews coefficient Solvent content 2.65 53.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.803 α = 90 b = 94.542 β = 90 c = 106.579 γ = 90
Symmetry Space Group P 21 21 21
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 2018-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0 ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) 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 2.3 47.27 99.8 0.084 0.991 7.4 3.7 39567
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 100 0.72 0.57 1.5 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 1Q5K 2.3 47.27 37543 1969 99.62 0.19483 0.19236 0.1981 0.24047 0.2406 RANDOM 37.707
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] -1.1 1.14 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.163 r_dihedral_angle_4_deg 20.277 r_dihedral_angle_3_deg 15.522 r_long_range_B_refined 7.996 r_long_range_B_other 7.993 r_dihedral_angle_1_deg 6.522 r_scangle_other 5.098 r_mcangle_it 4.549 r_mcangle_other 4.548 r_scbond_it 3.157
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.163 r_dihedral_angle_4_deg 20.277 r_dihedral_angle_3_deg 15.522 r_long_range_B_refined 7.996 r_long_range_B_other 7.993 r_dihedral_angle_1_deg 6.522 r_scangle_other 5.098 r_mcangle_it 4.549 r_mcangle_other 4.548 r_scbond_it 3.157 r_scbond_other 3.157 r_mcbond_it 2.807 r_mcbond_other 2.807 r_angle_refined_deg 1.386 r_angle_other_deg 0.994 r_chiral_restr 0.066 r_bond_refined_d 0.009 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 r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5580 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing