6HK7

Crystal structure of GSK-3B in complex with pyrazine inhibitor C50


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4ACD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.42930.2M potassium fluoride 22% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.0759.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.979α = 90
b = 103.727β = 90
c = 108.92γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2018-05-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1ELETTRA5.2R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
1351.8699.50.2810.3120.1330.9734.95.410015
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.1898.81.0611.1660.4780.755.7

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 REPLACEMENTTHROUGHOUT4ACD3.246.87785641299.430.204360.200040.28552RANDOM47.85
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]
-6.281.574.7
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_bonded60.459
r_sphericity_free41.663
r_dihedral_angle_2_deg35.703
r_dihedral_angle_4_deg20.75
r_dihedral_angle_3_deg17.574
r_long_range_B_refined17.498
r_long_range_B_other17.497
r_mcangle_it13.905
r_mcangle_other13.902
r_scangle_other12.62
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_bonded60.459
r_sphericity_free41.663
r_dihedral_angle_2_deg35.703
r_dihedral_angle_4_deg20.75
r_dihedral_angle_3_deg17.574
r_long_range_B_refined17.498
r_long_range_B_other17.497
r_mcangle_it13.905
r_mcangle_other13.902
r_scangle_other12.62
r_rigid_bond_restr10.933
r_mcbond_it10.077
r_mcbond_other10.068
r_scbond_it9.42
r_scbond_other9.417
r_dihedral_angle_1_deg6.515
r_angle_refined_deg1.717
r_angle_other_deg1.062
r_chiral_restr0.085
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2615
Nucleic Acid Atoms
Solvent Atoms1
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing