Experiment: 3R7R

Structure-based design of thienobenzoxepin inhibitors of PI3-Kinase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3E8X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	289	PEG 3350, 0.2M NH4SO4, 0.1M Tris-HCl 8.5, vapor diffusion, hanging drop, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.792	α = 90
b = 67.868	β = 95.4
c = 106.933	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		CCD	MAR		2007-05-17		SINGLE
2	1	x-ray		CCD	ADSC		2007-11-06		SINGLE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.0	ALS	5.0.2
2			1.0

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	2.5	50	98.6	0.042	15.7	2.8		34114

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	2.5	2.59	94.6		0.549		2.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	3e8x	2.9	19.927	1.34	22879	1179	99.7	0.2094	0.207	0.2017	0.2531	0.2465

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]
3.6067		7.4414	2.6581		-6.2648

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.955
f_angle_d	1.562
f_chiral_restr	0.116
f_bond_d	0.011
f_plane_restr	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6775
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	29

Software

Software
Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction