2X6J

THE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS34 IN COMPLEX WITH PIK-93

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2X6H	PDB ENTRY 2X6H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		PROTEIN WAS CRYSTALLISED IN 0.88M AMMONIUM SULPHATE, 100MM DI-POTASSIUM HYDROGEN PHOSPHATE AND 100MM DI-SODIUM HYDROGEN PHOSPHATE (TITRATED TO PH 7.5 WITH ORTHOPHOSPHORIC ACID). PROTEIN WAS SOAKED WITH 0.5MM PIK-93 IN MOTHER LIQUOR.

Crystal Properties
Matthews coefficient	Solvent content
4.15	70.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.95	α = 90
b = 156.33	β = 90
c = 242.91	γ = 90

Symmetry
Space Group	I 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	CCD	ADSC QUANTUM 315r		2009-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1		ESRF	ID23-1

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	3.5	72.28	99.7	0.11	4.8	3.52		26700		1.2

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	3.5	3.69	99.9		0.45	1.18	3.64

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2X6H	3.5	61.62	25387	1313	99.5	0.232	0.23	0.272	RANDOM	66.27

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]
0.36			3.02		-3.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.51
r_dihedral_angle_1_deg	25.4
r_dihedral_angle_3_deg	22.196
r_dihedral_angle_4_deg	18.957
r_scangle_it	2.049
r_angle_refined_deg	1.658
r_mcangle_it	1.258
r_scbond_it	1.128
r_mcbond_it	0.755
r_symmetry_vdw_refined	0.665
r_symmetry_hbond_refined	0.431
r_nbtor_refined	0.33
r_nbd_refined	0.295
r_xyhbond_nbd_refined	0.231
r_chiral_restr	0.11
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_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	8919
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing