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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 8 281 14% w/v PEG 10,000; 100mM Imidazole; pH 8 2 VAPOR DIFFUSION, SITTING DROP 7 281 18 % w/v PEG 8,000; 500 mM Lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.33 47.11 2.33 47.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.211 α = 84.01 b = 38.259 β = 87.43 c = 147.63 γ = 76.62
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 16M 2025-09-08 M SINGLE WAVELENGTH 2 2 93 PIXEL DECTRIS EIGER X 4M 2025-09-17
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97192 PETRA III, EMBL c/o DESY P13 (MX1) 2 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.97192 ESRF MASSIF-3
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 48.98 92.1 0.072 0.078 0.029 0.998 13.4 6.7 73204
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 72 1.008 1.099 0.43 0.599 6
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 2 48.98 50673 2664 97.59 0.29523 0.29205 0.3077 0.35355 0.3525 RANDOM 39.722
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] -1.8 0.03 -0.04 -1.43 -1.25 3.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.785 r_dihedral_angle_2_deg 9.903 r_long_range_B_refined 8.369 r_long_range_B_other 8.368 r_dihedral_angle_1_deg 8.125 r_scangle_other 5.812 r_mcangle_it 5.333 r_mcangle_other 5.333 r_scbond_it 3.622 r_scbond_other 3.622
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.785 r_dihedral_angle_2_deg 9.903 r_long_range_B_refined 8.369 r_long_range_B_other 8.368 r_dihedral_angle_1_deg 8.125 r_scangle_other 5.812 r_mcangle_it 5.333 r_mcangle_other 5.333 r_scbond_it 3.622 r_scbond_other 3.622 r_mcbond_it 3.449 r_mcbond_other 3.449 r_angle_refined_deg 1.773 r_angle_other_deg 0.559 r_chiral_restr 0.076 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 6056 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 196
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction