9Q74 | pdb_00009q74

Crystal structure of T. brucei EIF4E5 in complex with EIF4G1 peptide and cap-4.

X-RAY DIFFRACTION

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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 9.4 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 0.12 M monosaccharides (D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-Glucosamine), 0.1 M buffer system 1 pH 6.5 (imidazole, MES), 30% precipitant Mix2 (ethylene glycol, PEG 8000) from Morpheus Screen

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 140.38	α = 90
b = 140.38	β = 90
c = 41.35	γ = 120

Symmetry
Space Group	P 3 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 EIGER X 9M		2023-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.98011	SOLEIL	PROXIMA 2

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	1.57	121.57	94.4	0.999	11.3	7.1		39727

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	1.57	1.8			0.654

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	1.57	22.33	37673	2027	60.55	0.14444	0.14239	0.1519	0.18258	0.1865	RANDOM	22.815

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]
-1.11	-0.55		-1.11		3.59

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	30.464
r_long_range_B_other	29.063
r_scangle_other	22.47
r_mcangle_other	16.384
r_mcangle_it	16.374
r_scbond_it	15.258
r_scbond_other	15.253
r_dihedral_angle_3_deg	13.864
r_mcbond_it	10.797
r_mcbond_other	10.703
r_dihedral_angle_2_deg	8.662
r_rigid_bond_restr	7.871
r_dihedral_angle_1_deg	6.619
r_angle_refined_deg	1.81
r_angle_other_deg	0.59
r_chiral_restr	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1783
Nucleic Acid Atoms
Solvent Atoms	237
Heterogen Atoms	160

Software

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