4ANX | pdb_00004anx

Complexes of PI3Kgamma with isoform selective inhibitors.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		IN-HOUSE PI3KG STRUCTURE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	292	CRYSTALS WERE GROWN AT 19C IN HANGING DROPS USING VAPOR DIFFUSION. THE COMPLEX WAS FORMED BY INCUBATING 49.5UL OF PI3KG-HIS6 (7.2 MG/ML IN 20 MM TRIS-HCL, PH 7.2, 50 MM (NH4)2SO4, AND 1 MM TCEP) WITH 0.5UL OF LIGAND (100 MM STOCK IN 100% DMSO) FOR 30 MINUTES AT 4C. CRYSTALS OF THE BINARY COMPLEX WERE OBTAINED BY MIXING 1.0UL OF THE PI3KG:INHIBITOR COMPLEX WITH 1.0UL OF A RESERVOIR SOLUTION CONSISTING OF 16-21% PEG 4K, 0.25 M (NH4)2SO4, AND 0.1 M TRIS-HCL, PH 7.5.

Crystal Properties
Matthews coefficient	Solvent content
2.32	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.424	α = 90
b = 68.531	β = 95.26
c = 106.263	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	155	CCD	ADSC QUANTUM 315r		2010-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1		SSRL	BL7-1

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	2.73	32.6	99.4	0.08	14.3	3.7		27406		-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	2.73	3.07	99.4		0.77	1.8	3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	IN-HOUSE PI3KG STRUCTURE	2.73	32.6	26019	1375	99.45	0.22771	0.22472	0.23	0.28187	0.28	RANDOM

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]
0.01		0.07	0.04		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.075
r_dihedral_angle_3_deg	19.999
r_dihedral_angle_4_deg	15.206
r_dihedral_angle_1_deg	7.916
r_scangle_it	2.409
r_scbond_it	1.682
r_angle_refined_deg	1.601
r_mcangle_it	1.277
r_angle_other_deg	0.996
r_mcbond_it	0.943
r_nbd_refined	0.26
r_symmetry_vdw_other	0.245
r_nbd_other	0.217
r_nbtor_refined	0.199
r_xyhbond_nbd_refined	0.196
r_symmetry_vdw_refined	0.137
r_xyhbond_nbd_other	0.098
r_chiral_restr	0.094
r_nbtor_other	0.093
r_symmetry_hbond_refined	0.085
r_mcbond_other	0.081
r_bond_refined_d	0.014
r_bond_other_d	0.006
r_gen_planes_refined	0.005
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6757
Nucleic Acid Atoms
Solvent Atoms	34
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing