4DK5

Crystal structure of human PI3K-gamma in complex with a pyridyl-triazine inhibitor

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
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
Matthews coefficient	Solvent content
2.39	48.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.775	α = 90
b = 68.233	β = 94.99
c = 107.182	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	MARMOSAIC 225 mm CCD		2009-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.0000	APS	22-BM

Data Collection

Overall
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
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
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	R-Free	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	0.2891	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
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

RMS Deviations
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
r_nbd_refined	0.194
r_xyhbond_nbd_refined	0.133
r_symmetry_vdw_refined	0.127
r_symmetry_hbond_refined	0.068
r_chiral_restr	0.067
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6757
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms	49

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
EPMR	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.