5K5N

Crystal structure of GSK-3beta complexed with PF-04802367, a highly selective brain-penetrant kinase inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5295Protein storage conditions: 20 mM Tris pH 7.8, 5% (v/v) glycerol, 200 mM NaCl, 1 mM TCEP, 0.5 mM EDTA, 0.5% DMSO, and 0.2 mM PF-4802367, Well solution: 18-23% (w/v) PEG MME 5000, 100-150 mM ammonium sulfate, and 100 mM MES pH 6.5, Crystallization set-up: 0.5 + 0.5 uL drops over a well-solution of 200 uL
Crystal Properties
Matthews coefficientSolvent content
2.6854.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.293α = 90
b = 99.907β = 102.9
c = 66.91γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 3152008-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-BM1.00APS17-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.155095113.94418051.32
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.2160.60.4662.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.227.0342197212197.750.20510.20380.2287RANDOM58
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]
-0.34641.0771-0.32810.6745
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion17.44
t_omega_torsion2.7
t_angle_deg0.99
t_bond_d0.009
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion17.44
t_omega_torsion2.7
t_angle_deg0.99
t_bond_d0.009
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5243
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms60

Software

Software
Software NamePurpose
BUSTERrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
REFMACphasing