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Crystal structure of T. cruzi 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, HANGING DROP 291 Complex at 16 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 0.29 M (NH4)2SO4; 0.1 M Tris-HCl pH 8.5; 26% (m/V) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.54 51.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.38 α = 90 b = 88.889 β = 90 c = 110.165 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 2023-12-07 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 1.77 69.18 95.8 0.999 16.7 13.9 67238
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 1.77 1.9 0.773
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 1.77 25.21 63798 3398 78.95 0.16052 0.15763 0.1798 0.21501 0.2303 RANDOM 26.597
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] -0.46 -5.25 5.71
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 28.974 r_long_range_B_other 28.317 r_scangle_other 25.003 r_scbond_it 19.513 r_scbond_other 19.447 r_mcangle_other 13.436 r_mcangle_it 13.432 r_dihedral_angle_2_deg 13.414 r_dihedral_angle_3_deg 13.039 r_mcbond_it 9.077
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 28.974 r_long_range_B_other 28.317 r_scangle_other 25.003 r_scbond_it 19.513 r_scbond_other 19.447 r_mcangle_other 13.436 r_mcangle_it 13.432 r_dihedral_angle_2_deg 13.414 r_dihedral_angle_3_deg 13.039 r_mcbond_it 9.077 r_mcbond_other 9.049 r_rigid_bond_restr 7.659 r_dihedral_angle_1_deg 6.427 r_angle_refined_deg 1.506 r_angle_other_deg 0.542 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 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 5493 Nucleic Acid Atoms Solvent Atoms 572 Heterogen Atoms 265
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction autoPROC data processing Aimless data scaling MOLREP phasing XDS data reduction