2WXG | pdb_00002wxg

The crystal structure of the murine class IA PI 3-kinase p110delta in complex with SW13.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2RD0	PDB ENTRY 2RD0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.8		20% (V/V) GLYCEROL, 10% (W/V) PEG 4K, 30 MM NANO3, 30 MM NA2HPO4, 30 MM (NH4)2SO4, 100 MM IMIDAZOLE PH 6.8

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.761	α = 90
b = 64.675	β = 102.95
c = 116.721	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	ADSC CCD		2008-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	69.01	99.8	0.09	15.69	7.38		69666		-3.7	31.443

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	2.02	100		0.72	1.82	7.44

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	PDB ENTRY 2RD0	2	113.96	67557	2108	99.75	0.20724	0.2061	0.21	0.24343	0.25	RANDOM	24.549

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]
0.33		-0.07	0.14		-0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.775
r_dihedral_angle_4_deg	17.672
r_dihedral_angle_3_deg	16.562
r_dihedral_angle_1_deg	5.489
r_scangle_it	3.421
r_scbond_it	2.149
r_angle_refined_deg	1.341
r_mcangle_it	1.332
r_mcbond_it	0.701
r_nbtor_refined	0.305
r_symmetry_hbond_refined	0.287
r_symmetry_vdw_refined	0.244
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.095
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
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	6739
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms	38

Software

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