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) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1Q5K |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | GSK3beta(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 | |
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Matthews coefficient | Solvent content |
2.65 | 53.54 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 86.803 | ¦Á = 90 |
b = 94.542 | ¦Â = 90 |
c = 106.579 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 100 | PIXEL | DECTRIS PILATUS 2M | 2018-01-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ELETTRA BEAMLINE 5.2R | 1.0 | ELETTRA | 5.2R |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rpim I (All) | CC (Half) | 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 | 2.3 | 47.27 | 99.8 | 0.084 | 0.991 | 7.4 | 3.7 | 39567 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.3 | 2.38 | 100 | 0.72 | 0.57 | 1.5 | 3.8 |
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1Q5K | 2.3 | 47.27 | 37543 | 1969 | 99.62 | 0.19483 | 0.19236 | 0.24047 | RANDOM | 37.707 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-1.1 | 1.14 | -0.04 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.163 |
r_dihedral_angle_4_deg | 20.277 |
r_dihedral_angle_3_deg | 15.522 |
r_long_range_B_refined | 7.996 |
r_long_range_B_other | 7.993 |
r_dihedral_angle_1_deg | 6.522 |
r_scangle_other | 5.098 |
r_mcangle_it | 4.549 |
r_mcangle_other | 4.548 |
r_scbond_it | 3.157 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5580 |
Nucleic Acid Atoms | |
Solvent Atoms | 266 |
Heterogen Atoms | 76 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |