Experiment: 9Q79

Crystal structure of T. cruzi EIF4E6 in complex with EIF4G5 peptide and cap-4

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	Complex at 7.3 mg/mL in 20 mM Tris-HCl, 150 mM NaCl, 2 mM DTT, pH 8.0 (pre-incubated with cap-4) with crystallization buffer containing 100 mM tri-sodium citrate (pH 3.5) and 20.6% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.211	α = 90
b = 93.236	β = 90
c = 119.649	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS 6M		2024-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.97856	SOLEIL	PROXIMA 1

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	2.3	119.65	96.1	0.998	8.6	13.5		30384

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	2.3	2.39			0.782

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	THROUGHOUT	2.3	46.62	1.36	30338	1558	73.93	0.2376	0.234	0.2339	0.3044	0.3045

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	19.189
f_angle_d	1.24
f_chiral_restr	0.051
f_bond_d	0.009
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6648
Nucleic Acid Atoms
Solvent Atoms	148
Heterogen Atoms	253

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
autoPROC	data processing
Aimless	data scaling
MOLREP	phasing
XDS	data reduction