8FH4 | pdb_00008fh4

Crystal structure of HPK1 kinase domain T165E,S171E phosphomimetic mutant in complex with 3-[6-chloro-4-(9-methyl-1-oxa-4,9-diazaspiro[5.5]undec-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl]benzonitrile

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6NG0	PDB entry 6NG0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		286.15	15 mg/mL protein + reservoir (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
2.2	44.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.756	α = 97.66
b = 70.505	β = 108.73
c = 86.042	γ = 92.66

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		2016-03-02	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 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	1.83	69.56	82.6	0.03	0.042	0.03	0.996	9.7	1.8		92890

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.83	1.93	25		0.292	0.292	0.833	1.9	1.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB entry 6NG0	1.827	69.56	92889	4440	82.6	0.1888	0.1874	0.18	0.2152	0.21	RANDOM	31.69

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]
1.4506	0.1642	2.3978	-4.8007	1.1515	3.3501

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	17.32
t_omega_torsion	2.99
t_angle_deg	0.91
t_bond_d	0.008
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9114
Nucleic Acid Atoms
Solvent Atoms	834
Heterogen Atoms	125

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	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.