5XGJ

Crystal structure of PI3K complex with an inhibitor

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291.15	0.15M Lithium sulfate, 0.1M Tris-HCl pH 8.5, 28%(W/V) PEG2000MME

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.877	α = 90
b = 136.368	β = 90
c = 149.028	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CMOS	DECTRIS PILATUS3 S 6M		2016-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	1	SSRF	BL19U1

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	2.97	50	99	0.157	10.64	6		29684

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.98	3.09	98.2		2.25	5.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.97	50	28231	1400	98.58	0.23341	0.2311	0.27917	RANDOM	98.564

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]
1.3			-5.4		4.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.101
r_dihedral_angle_3_deg	13.047
r_dihedral_angle_4_deg	12.706
r_dihedral_angle_1_deg	5.171
r_long_range_B_refined	4.729
r_long_range_B_other	4.729
r_mcangle_it	2.905
r_mcangle_other	2.904
r_scangle_other	2.31
r_mcbond_it	1.64
r_mcbond_other	1.64
r_scbond_it	1.259
r_scbond_other	1.258
r_angle_refined_deg	0.96
r_angle_other_deg	0.814
r_chiral_restr	0.053
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10371
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
SCALEPACK	data scaling
PHASER	phasing