4WWN | pdb_00004wwn

Crystal structure of human PI3K-gamma in complex with (S)-N-(1-(7-fluoro-2-(pyridin-2-yl)quinolin-3-yl)ethyl)-9H-purin-6-amine AMG319 inhibitor

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	298	21% PEG 3350, 100 mM Tris (pH 7.3), 245 mM ammonium sulfate, 1 mM dithiothreitol, 1 mM EDTA

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.873	α = 90
b = 68.213	β = 94.81
c = 106.69	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	IMAGE PLATE	RIGAKU RAXIS IV++		2008-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

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	2.7	30	95.3	0.076	16	2.4	28575	27232		-3	83.6

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	2.7	2.8	96.4		0.399		2.2	2728

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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		THROUGHOUT	2.7	30	27231	1951	95.21	0.2213	0.216	0.22	0.2907	0.29	RANDOM	71.3

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]
-3.05		0.06	2.55		0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.116
r_dihedral_angle_3_deg	16.153
r_dihedral_angle_4_deg	15.772
r_dihedral_angle_1_deg	5.983
r_angle_refined_deg	1.139
r_angle_other_deg	0.821
r_chiral_restr	0.062
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.116
r_dihedral_angle_3_deg	16.153
r_dihedral_angle_4_deg	15.772
r_dihedral_angle_1_deg	5.983
r_angle_refined_deg	1.139
r_angle_other_deg	0.821
r_chiral_restr	0.062
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6729
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms	39

Software

Software
Software Name	Purpose
CrystalClear	data collection
DENZO	data reduction
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
REFMAC	refinement

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.