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Crystal structure of human glycogen synthase kinase 3 beta (GSK3b) in complex with inhibitor 142
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JLD PDB ENTRY 2JLD chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 296 20% PEG3350, 0.1M sodium Hepes pH 7.0, 2% (v/v) Tacsimate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.61 52.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.52 α = 90 b = 110.78 β = 97.08 c = 67.91 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 6M Oxford Danfysik/SESO Two stage demagnification using two K-B pairs of bimorph type mirrors 2010-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9778 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 2.231 46.14 99 0.1 0.1 7.1 3.7 46924 46924 1 1 41.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.231 2.3 99.7 0.561 0.561 2.5 3.8 3465
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 PDB ENTRY 2JLD chain A 2.231 46.14 44525 2373 97.18 0.20189 0.20041 0.1988 0.22983 0.2251 RANDOM 40.111
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] -3.64 -11.31 9.63 -5.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.929 r_dihedral_angle_4_deg 22.291 r_dihedral_angle_3_deg 16.289 r_dihedral_angle_1_deg 5.98 r_scangle_it 3.227 r_scbond_it 1.973 r_angle_refined_deg 1.592 r_mcangle_it 1.564 r_mcbond_it 0.85 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.929 r_dihedral_angle_4_deg 22.291 r_dihedral_angle_3_deg 16.289 r_dihedral_angle_1_deg 5.98 r_scangle_it 3.227 r_scbond_it 1.973 r_angle_refined_deg 1.592 r_mcangle_it 1.564 r_mcbond_it 0.85 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5474 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 83
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling