2EC8

Crystal structure of the exctracellular domain of the receptor tyrosine kinase, Kit

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	277	12% PEG 400, 0.2M KCl, 0.1M Na-Pi buffer, pH 6.0, VAPOR DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 162.249	α = 90
b = 162.249	β = 90
c = 67.586	γ = 120

Symmetry
Space Group	H 3

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 4		2006-04-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C	1.1000	NSLS	X26C

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	50	99.8	0.076	11.7	11.7	13342	13342

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	3.11	100		0.17	7.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MIRAS	THROUGHOUT	3	27.07	13189	12521	650	99.86	0.25638	0.25435	0.2731	0.29505	0.2757	RANDOM	31.821

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]
-0.76	-0.38		-0.76		1.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.886
r_dihedral_angle_3_deg	20.571
r_dihedral_angle_4_deg	12.511
r_dihedral_angle_1_deg	6.211
r_scangle_it	5.334
r_mcangle_it	4.056
r_scbond_it	3.596
r_mcbond_it	2.544
r_angle_refined_deg	1.848
r_symmetry_hbond_refined	0.357
r_nbtor_refined	0.339
r_symmetry_vdw_refined	0.334
r_nbd_refined	0.303
r_xyhbond_nbd_refined	0.162
r_chiral_restr	0.115
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3498
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	70

Software

Software
Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing
REFMAC	refinement