5T7F

PI3Kdelta in complex with the inhibitor GS-643624

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
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 mM Tris, 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 45 s, flash-frozen in liquid nitrogen, and stored at minus 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):idelalisib crystals started with a mixture of 0.48 microliters of 2.5% (w/v) n-dodecyl-(beta)-D-maltoside, 0.30 microliters of 20 mM ligand, and 12 microliters 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 microliters of 1% to 30% (v/v) PEG 300, 0.1 M Tris (pH 8.5) at 20 degrees C. Crystals appeared in 2 to 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
Matthews coefficient	Solvent content
2.7	54.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.226	α = 90
b = 142.794	β = 90.055
c = 221.067	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
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		2013-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	1.0	ALS	5.0.1

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	2.6	50	91.8	15.3	3.4		56178			52.15

Highest Resolution Shell
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	81.6		0.58	1.2	3

Refinement

Statistics
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	45.9	1.335	56149	1983	91.36	0.23	0.23	0.294	63.31

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.983972498
f_angle_d	0.775965310742
f_chiral_restr	0.031067372862
f_bond_d	0.00395315120515
f_plane_restr	0.00303656179063

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13178
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	66

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
EPMR	phasing