6NG0 | pdb_00006ng0

Crystal structure of HPK1 kinase domain T165E,S171E phosphomimetic mutant in complex with sunitinib in the inactive state.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	286.15	200 nl protein (15 mg/ml) plus 300 nl reservoir solution (0.1 M tris, pH 8.0, 17.5 % 1,6-Hexanediol, 10 mM magnesium sulfate, 24 mM Barium acetate)

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.81	α = 82.44
b = 58.92	β = 82.31
c = 60.93	γ = 64.34

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	180	PIXEL	DECTRIS PILATUS3 6M		2018-08-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.000	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.026	60.176	97.3	0.036	0.999	14.9	3.6		43684			44.17

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.026	2.061	96.1		0.501	0.872		3.7

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.05	27.69	42208	2160	97.3	0.202	0.201	0.2	0.229	0.23	RANDOM	57.77

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]
-8.1079	-7.9928	6.0821	-0.5908	-8.1366	8.6987

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	16.71
t_omega_torsion	2.76
t_angle_deg	0.99
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	16.71
t_omega_torsion	2.76
t_angle_deg	0.99
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	4336
Nucleic Acid Atoms
Solvent Atoms	320
Heterogen Atoms	58

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
PDB_EXTRACT	data extraction
XSCALE	data scaling
PHASER	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.