6HH1 | pdb_00006hh1

Structure of c-Kit with allosteric inhibitor 3G8

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	293	9.3 mg/mL protein in 250 mM NaCl, 25 mM Tris-HCl pH 7.4, 1 mM EDTA, 0.5 mM TCEP, 1.2 mM 3G8, 0.1% w/w V8 protease. 800 nL of protein was mixed with 800 nL of crystallization solution (0.1 M Tris-HCl pH 9.1, 1.5 M diammonium hydrogen phosphate) and incubated over 0.4 mL crystallization solution in 24 well VDX plates. Crystals were cryo-protected with 20% v/v ethylene glycol.

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.614	α = 90
b = 65.614	β = 90
c = 159.004	γ = 120

Symmetry
Space Group	P 32 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 315r		2012-09-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.976	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	20	97.65	0.13	5.42	3.94		21244		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.27	99.81		0.8	1.6	4.05

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	2.25	25.32	17585	940	94.72	0.208	0.2045	0.21	0.2734	0.27	RANDOM	62.078

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]
-0.94	-0.47		-0.94		3.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.871
r_dihedral_angle_4_deg	23.022
r_dihedral_angle_3_deg	18.937
r_dihedral_angle_1_deg	6.868
r_angle_refined_deg	1.896
r_angle_other_deg	1.321
r_chiral_restr	0.087
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_gen_planes_other	0.007
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2400
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling