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