4DK5
Crystal structure of human PI3K-gamma in complex with a pyridyl-triazine inhibitor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1E8Y | PDB entry 1E8Y |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.3 | 273 | 21% polyethylene glycol 3350, 100 mM Tris, 245 mM ammonium sulfate, 1 mM DTT, 2 mM EDTA, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 273K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.39 | 48.44 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 143.775 | α = 90 |
b = 68.233 | β = 94.99 |
c = 107.182 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 100 | CCD | MARMOSAIC 225 mm CCD | 2009-02-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-BM | 1.0000 | APS | 22-BM |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.95 | 50 | 99.8 | 0.075 | 10.1 | 3.4 | 22189 | 22145 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.95 | 3.06 | 99.6 | 0.737 | 3.3 | 2186 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1E8Y | 2.95 | 50 | 22050 | 21966 | 1584 | 99.62 | 0.2239 | 0.2188 | 0.21 | 0.2891 | 0.27 | RANDOM | 87.3493 |
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] | |
-1.85 | 0.77 | 2.85 | -0.86 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.758 |
r_dihedral_angle_3_deg | 17.067 |
r_dihedral_angle_4_deg | 15.327 |
r_dihedral_angle_1_deg | 5.167 |
r_scangle_it | 1.071 |
r_angle_refined_deg | 1.002 |
r_mcangle_it | 0.937 |
r_scbond_it | 0.657 |
r_mcbond_it | 0.521 |
r_nbtor_refined | 0.302 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6757 |
Nucleic Acid Atoms | |
Solvent Atoms | 14 |
Heterogen Atoms | 49 |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
EPMR | phasing |