5K5N
Crystal structure of GSK-3beta complexed with PF-04802367, a highly selective brain-penetrant kinase inhibitor
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 295 | Protein 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 | |
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Matthews coefficient | Solvent content |
2.68 | 54.07 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 66.293 | α = 90 |
b = 99.907 | β = 102.9 |
c = 66.91 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 93 | CCD | ADSC QUANTUM 315 | 2008-02-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-BM | 1.00 | APS | 17-BM |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.15 | 50 | 95 | 11 | 3.9 | 44180 | 51.32 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.15 | 2.21 | 60.6 | 0.466 | 2.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | 2.2 | 27.03 | 42197 | 2121 | 97.75 | 0.2051 | 0.2038 | 0.2287 | RANDOM | 58 |
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] | |
-0.3464 | 1.0771 | -0.3281 | 0.6745 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 17.44 |
t_omega_torsion | 2.7 |
t_angle_deg | 0.99 |
t_bond_d | 0.009 |
t_dihedral_angle_d | |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_trig_c_planes | |
t_gen_planes | |
t_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5243 |
Nucleic Acid Atoms | |
Solvent Atoms | 149 |
Heterogen Atoms | 60 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
PDB_EXTRACT | data extraction |
REFMAC | phasing |