Experiment: 10JU

Crystal Structure of serine/threonine-protein kinase (AEK1) T376D, S395D Mutant from Trypanosoma brucei (AMP-PNP)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9Z8K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	Index F6 0.2M Ammonium sulfate 0.1M Bis-Tris pH 5.5 25% PEG 3350. TrbrA.01480.a.WW4.PS38793 at 13.5 mg/mL. The C-terminal tail ~60 residues was disordered in each subunit. Residue Ser 71 in subunit A contained a large amount of density near the OG atom. This was modeled as a phosphoserine (SEP) although this is not a predicted phosphorylation site. 2mM AMP-PNP and 2mM MgCl2 added prior to crystallization. Prominent AMP-PNP density in subunit B but disorder in the phosphate portion. plate 20522 F6 drop 2, Puck: PSL-0904, Cryo: 80% crystallant + 20% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.538	α = 90
b = 88.475	β = 90
c = 201.132	γ = 90

Symmetry
Space Group	I 2 2 2

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		2025-12-13	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	2.15	44.24	100	0.079	0.082	0.023	0.999	17.2	13.3		42374

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	2.15	2.22		100	1.693	1.758	0.473	0.747		13.7

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	2.15	44.24	1.34	42358	2230	99.96	0.2202	0.2186	0.2208	0.2504	0.2458

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	15.349
f_angle_d	0.641
f_chiral_restr	0.047
f_plane_restr	0.006
f_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4104
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms	86

Software

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