9D00 | pdb_00009d00

HPK1 kinase domain T165E,S171E phosphomimetic mutant in complex with compound 53

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		286.15	Well Ingredients: Buffer: 0.1 M (2.5 uL of stock 1.0 M) Tris (pH 8.00) Salt: 0.01 M (0.5 uL of stock 0.5 M) Magnesium sulfate hydrate Precipitant: 21.0 %w/v (7.3943661972 uL of stock 71.0 %w/v) 1,6 hexanediol Additive: 0.036 M (9.0 uL of stock 0.1 M) Barium Acetate Plate setup temperature: 13 C Plate incubation temperature: 13 C Drop volume from well: 0.3 uL Drop protein volume: 0.2 uL Protein concentration 15mg/ml

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.78	α = 103.45
b = 80.33	β = 106.49
c = 84.09	γ = 103.18

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	95	PIXEL	DECTRIS EIGER2 S 9M		2020-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.0000	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.95	76.43	84.5	0.996	10	3.5		66808

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.11			0.555

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	1.951	33.34	66792	3298	69.8	0.2474	0.2457	0.2414	0.2791	0.2711	RANDOM	57.29

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]
-3.6006	-4.108	-0.7852	4.8049	1.6708	-1.2043

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	17.49
t_omega_torsion	2.83
t_angle_deg	0.91
t_bond_d	0.008
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	17.49
t_omega_torsion	2.83
t_angle_deg	0.91
t_bond_d	0.008
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	8985
Nucleic Acid Atoms
Solvent Atoms	528
Heterogen Atoms	120

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
STARANISO	data scaling
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.