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Homo sapiens Eukaryotic translation initiation factor 4E (eIF4E) in complex with synthetic mRNA cap analogs
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IPB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 281 18 % w/v PEG 10,000; 20 % w/v Glycerol; 100 mM TRIS; pH 8.5; 100 mM Sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.04 39.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.042 α = 90 b = 128.493 β = 97.31 c = 71.634 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 PIXEL DECTRIS EIGER X 4M 2025-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96770 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.75 42.83 98.9 0.155 0.161 0.042 0.999 10 14.4 71323
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 98.9 2.487 2.575 0.663 0.564 14.7
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 1.75 42.38 67740 3566 98.8 0.20725 0.20559 0.2168 0.23866 0.2428 RANDOM 30.238
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] -0.39 0.73 -1.51 1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.555 r_long_range_B_other 7.638 r_long_range_B_refined 7.636 r_dihedral_angle_2_deg 7.397 r_dihedral_angle_1_deg 6.817 r_scangle_other 6.071 r_mcangle_it 3.882 r_mcangle_other 3.882 r_scbond_it 3.858 r_scbond_other 3.858
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.555 r_long_range_B_other 7.638 r_long_range_B_refined 7.636 r_dihedral_angle_2_deg 7.397 r_dihedral_angle_1_deg 6.817 r_scangle_other 6.071 r_mcangle_it 3.882 r_mcangle_other 3.882 r_scbond_it 3.858 r_scbond_other 3.858 r_mcbond_it 2.688 r_mcbond_other 2.687 r_angle_refined_deg 1.647 r_angle_other_deg 0.536 r_chiral_restr 0.079 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5983 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 288
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction