6PYU | pdb_00006pyu

Human PI3Kdelta in complex with Compound 4-2 ((3S)-1'-(cyclopropanecarbonyl)-5-(quinoxalin-6-yl)spiro[indole-3,2'-pyrrolidin]-2(1H)-one)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	not available

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.439	α = 90
b = 108.587	β = 90
c = 142.279	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	PIXEL	DECTRIS PILATUS 6M		2015-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.000	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	2.54	86.39	98.1	0.093	0.102	0.992	11.78	6		46030			79.269

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.54	2.79	98.4		0.987	0.11	0.985	18.3	5.9

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	FOURIER SYNTHESIS	THROUGHOUT	2.54	86.39	45628	955	98.95	0.2408	0.2397	0.24	0.2916	0.29	RANDOM	106.112

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]
3.9			3.09		-6.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.246
r_dihedral_angle_4_deg	15.444
r_dihedral_angle_3_deg	13.907
r_dihedral_angle_1_deg	5.732
r_angle_refined_deg	1.214
r_angle_other_deg	0.898
r_chiral_restr	0.067
r_bond_refined_d	0.009
r_bond_other_d	0.005
r_gen_planes_refined	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.246
r_dihedral_angle_4_deg	15.444
r_dihedral_angle_3_deg	13.907
r_dihedral_angle_1_deg	5.732
r_angle_refined_deg	1.214
r_angle_other_deg	0.898
r_chiral_restr	0.067
r_bond_refined_d	0.009
r_bond_other_d	0.005
r_gen_planes_refined	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8886
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

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.