6H0U

Glycogen synthase kinase-3 beta (GSK3) complex with a covalent [1,2,4]triazolo[1,5-a][1,3,5]triazine inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q5K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7293GSK3beta(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 coefficientSolvent content
2.6553.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.803α = 90
b = 94.542β = 90
c = 106.579γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2018-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1.0ELETTRA5.2R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.347.2799.80.0840.9917.43.739567
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.381000.720.571.53.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1Q5K2.347.2737543196999.620.194830.192360.24047RANDOM37.707
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]
-1.11.14-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.163
r_dihedral_angle_4_deg20.277
r_dihedral_angle_3_deg15.522
r_long_range_B_refined7.996
r_long_range_B_other7.993
r_dihedral_angle_1_deg6.522
r_scangle_other5.098
r_mcangle_it4.549
r_mcangle_other4.548
r_scbond_it3.157
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.163
r_dihedral_angle_4_deg20.277
r_dihedral_angle_3_deg15.522
r_long_range_B_refined7.996
r_long_range_B_other7.993
r_dihedral_angle_1_deg6.522
r_scangle_other5.098
r_mcangle_it4.549
r_mcangle_other4.548
r_scbond_it3.157
r_scbond_other3.157
r_mcbond_it2.807
r_mcbond_other2.807
r_angle_refined_deg1.386
r_angle_other_deg0.994
r_chiral_restr0.066
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms5580
Nucleic Acid Atoms
Solvent Atoms266
Heterogen Atoms76

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing