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Trypanosoma brucei EIF4E5 translation initiation factor in complex with 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, HANGING DROP 291 Protein at 7.5 mg/mL, in 20 mM Tris-HCl, 150 mM NaCl, 2 mM DTT, pH 8.0 (pre-incubated with cap-4) with crystallization solution containing 0.03 M Divalents, 0.1 M buffer system 1 (pH 6.5), 24% precipitant Mix, from Morpheus Screen
Crystal Properties Matthews coefficient Solvent content 3 59.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.66 α = 90 b = 72.66 β = 90 c = 95.26 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 EIGER X 9M 2022-12-12 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 1.25 37.98 96.1 0.999 23.1 19.9 80904
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 1.252 3.563 0.615
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 1.25 37.98 76755 4040 99.95 0.14067 0.13922 0.163 0.1689 0.1895 RANDOM 26.418
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] 0.92 0.46 0.92 -2.98
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 90.835 r_long_range_B_refined 90.59 r_scbond_it 78.621 r_scbond_other 78.586 r_rigid_bond_restr 20.159 r_dihedral_angle_3_deg 12.723 r_mcangle_it 10.224 r_mcangle_other 10.221 r_mcbond_it 7.164 r_mcbond_other 7.126
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 90.835 r_long_range_B_refined 90.59 r_scbond_it 78.621 r_scbond_other 78.586 r_rigid_bond_restr 20.159 r_dihedral_angle_3_deg 12.723 r_mcangle_it 10.224 r_mcangle_other 10.221 r_mcbond_it 7.164 r_mcbond_other 7.126 r_dihedral_angle_2_deg 7.076 r_dihedral_angle_1_deg 5.974 r_angle_refined_deg 1.884 r_angle_other_deg 0.643 r_chiral_restr 0.098 r_bond_refined_d 0.012 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_scangle_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1482 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 133
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction autoPROC data processing Aimless data scaling MOLREP phasing