5T8I
PI3Kdelta in complex with the inhibitor GS-9901
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 293 | Crystals used for seeding were obtained by vapor diffusion at 20 degrees C with 25 nl of 11 mg/ml (delta)ABD-p110(delta) and 0.9 mM of a p110(delta) inhibitor in protein storage buffer (20 mMTris, pH 7.2, 50 mM (NH4)2SO4, 1% v/v ethylene glycol, 1% (w/v) betaine, 0.3 microM CHAPS, and 5 mM TCEP) added to 25 nl of reservoir solution (25% (w/v) PEG 3350, 0.1 M bis-tris (pH 6.5). Crystals were pulverized, pooled together in the reservoir solution, vortexed with a Seed-Bead (Hampton Research) for 45s, flash-frozen in liquid nitrogen, and stored at -80 degrees C. For seeding crystallization trials, the frozen seed was thawed and diluted 500-fold in 25% (v/v) PEG 300, 0.1 M Tris (pH 8.5). Preparation of diffraction quality (delta)ABD-p110(delta):GS-9901 crystals started with a mixture of 0.48 microL of 2.5% (w/v) n-dodecyl-(beta)-D-maltoside, 0.30 microL of 20 mM ligand, and 12 microL of 12 mg/ml (delta)ABD-p110(delta) in storage buffer (described above). The mixture was allowed to sit for 1 h at room temperature instead of 4 degrees C to prevent the formation of white precipitate. Seeded vapor diffusion droplets were assembled by adding 90 nl of the 500-fold diluted seed (described above) to 100 nl of the n-dodecyl-(beta)-D-maltoside-ligand-(delta)ABD-p110(delta) mixture. The droplets were equilibrated against reservoir wells containing 50 microL of 1% to 30% (v/v) PEG 300, 0.1 M Tris (pH 8.5) at 20 degrees C. Crystals appeared in 2-5 days across the 1% to 30% PEG range. Crystals were cryoprotected in 20% (w/v) glycerol, 25% (w/v) PEG 300, 0.1 M Tris (pH 8.5), 50 mM ammonium sulfate, 0.2% (w/v) n-dodecyl-(beta)-D-maltoside, 0.2 mM ligand and were flash-frozen in liquid nitrogen for data collection. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.35 | 47.69 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.045 | α = 90 |
b = 142.197 | β = 90 |
c = 222.59 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | CCD | ADSC QUANTUM 315r | 2013-10-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | 1.00 | ALS | 5.0.1 |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.6 | 50 | 91.4 | 25.6 | 5.6 | 28814 | 69.98 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.6 | 2.64 | 89.8 | 0.646 | 1.8 | 5.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.6 | 45.88 | 1.347 | 28810 | 1999 | 91.25 | 0.256 | 0.252 | 0.3125 | 97.52 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 15.3512390715 |
f_angle_d | 0.703052666865 |
f_chiral_restr | 0.0276211715151 |
f_bond_d | 0.00307636183537 |
f_plane_restr | 0.00243354710326 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6508 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 34 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
EPMR | phasing |