10SL | pdb_000010sl

Crystal Structure of serine/threonine-protein kinase (AEK1) from Trypanosoma cruzi in complex with Hesperadin

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	10BL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	291	3.0M Sodium Malonate, pH 5.0. TrcrB.01480.a.WW4.PS38791 at 16.9 mg/mL. Cocrystallization with 4mM ATP and 4mM MgCl2. Crystals were soaked overnight in 10 mM Hespreadin solubilized in 3.0M Malonate, pH 5.0 which displaced the ATP. plate Liu-S-198, Puck: PSL-1705, Cryo: 3.0M Sodium Malonate

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.518	α = 90
b = 86.518	β = 90
c = 193.041	γ = 120

Symmetry
Space Group	P 31 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	100	PIXEL	DECTRIS EIGER2 XE 9M		2026-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 19-ID	0.9786	NSLS-II	19-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	2.72	48.82	99.9	0.139	0.143	0.032	0.999	18.8	20.1		23234

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	2.72	2.79		100	2.084	2.134	0.46	0.899		21.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.72	48.82	1.34	23100	1126	99.58	0.2254	0.2231	0.224	0.2689	0.2609

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.347
f_angle_d	0.573
f_chiral_restr	0.042
f_plane_restr	0.004
f_bond_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5325
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms	81

Software

Software
Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction