6D1Z | pdb_00006d1z

Crystal structure of Tyrosine-protein kinase receptor in complex with 5-(4-fluorophenyl)thieno[2,3-d]pyrimidin-4(3H)-one Inhibitor

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.63	294	Well volume: 30.0 uL Well Ingredients: Salt: 0.2571428571 M (1.9285714282 uL of stock 4.0 M) potassium formate Precipitant: 20.0 %w/v (12.0 uL of stock 50.0 %w/v) PEG 3350 Buffer: 0.1 M (3.0 uL of stock 1.0 M) Tris (pH 7.63) Plate setup temperature: 13 C Plate incubation temperature: 21 C Drop volume from well: 0.1 uL Drop protein volume: 0.3 uL Protein: 6.00 mg/mL (0.17 mM) Compound1: small molecule to aid crystallization (1.20 mM) Soak of 10mM compound 3 for > 1h into co-crystals of TrkA + compound1

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.15	α = 90
b = 45.66	β = 126.88
c = 78.88	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 6M		2013-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	1	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.87	39.15	97.6	0.109	0.131	0.072	0.978	9.7	3.2		26217			28.88

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.87	1.92	99.1		0.86	1.03	0.569	0.392		3.2

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	1.87	39.15	26216	1331	97.37	0.1797	0.1781	0.18	0.2096	0.21	RANDOM	32.38

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]
0.719		1.2437	0.2124		-0.9314

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	16.11
t_omega_torsion	3.14
t_angle_deg	0.95
t_bond_d	0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	16.11
t_omega_torsion	3.14
t_angle_deg	0.95
t_bond_d	0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
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	2316
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms	54

Software

Software
Software Name	Purpose
Aimless	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
BUSTER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.