Experiment: 7KHG

Crystal structure of KIT kinase domain with a small molecule inhibitor, PLX3397

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1T45

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	1.6M ammonium sulfate, 2.0M sodium Chloride and 0.1M Bis-Tris, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.93	58.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.133	α = 90
b = 81.961	β = 107.6
c = 50.061	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 QUANTUM 210		2006-03-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.1159	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.15	64.823	99.6	0.071	7.9	3.6		23250			32.53

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.27			0.419

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1T45	2.15	64.823	1.34	23250	2000	99.5	0.1837	0.1818	0.2033	0.2111	36.4077

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	19.203
f_angle_d	0.883
f_chiral_restr	0.056
f_bond_d	0.007
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2602
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms	29

Software

Software
Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
MOLREP	phasing