6DKI | pdb_00006dki

Crystal structure of Trk-A in complex with the Pan-Trk Kinase Inhibitor, compound 19.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	294	Well volume: 20.0 uL Well Ingredients: Polymer: 9.0 %w/v (3.6 uL of stock 50.0 %w/v) PEG 3350 Buffer: 15.8 %v/v (3.16 uL of stock 100.0 %v/v) tacsimate (pH 8.00) Additive: 0.025 M (5.0 uL of stock 0.1 M) TCEP hydrochloride Plate setup temperature: 13 C Plate incubation temperature: 21 C Drop volume from well: 0.01 uL Drop protein volume: 0.2 uL Protein: 6.30 mg/mL

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.64	α = 90
b = 45.51	β = 126.56
c = 79.32	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	93	PIXEL	DECTRIS PILATUS3 S 6M		2013-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.0	APS	17-ID

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	2.11	40.73	99	0.054	12.9	3.3		18843			37.38

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.11	2.22	99.7		0.396		3.3

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		THROUGHOUT	2.11	40.73	18784	966	98.84	0.186	0.1837	0.1844	0.227	0.2258	RANDOM	39.71

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]
-0.6636		-0.4987	1.4264		-0.7628

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	16.65
t_omega_torsion	3.2
t_angle_deg	0.97
t_bond_d	0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2252
Nucleic Acid Atoms
Solvent Atoms	97
Heterogen Atoms	49

Software

Software
Software Name	Purpose
BUSTER	refinement
SCALA	data scaling
Coot	model building
BUSTER	phasing