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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 7.5 281 32% w/v PEG 4000 100mM TRIS; pH 8.5 800 mM Lithium sulfate
Crystal Properties Matthews coefficient Solvent content 3.33 63.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.037 α = 90 b = 38.363 β = 100.46 c = 92.104 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 EIGER2 X CdTe 16M 2025-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.97630 PETRA III, EMBL c/o DESY P14 (MX2)
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 2 43.33 99.6 0.287 0.299 0.08 0.996 8 13.6 40448
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 2 2.05 99.8 2.744 2.85 0.76 0.467 13.7
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 2 42.3 38416 2022 99.5 0.213 0.212 0.2267 0.239 0.2524 RANDOM 36.64
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] -0.13 -1.07 -0.9 1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.481 r_long_range_B_other 11.048 r_long_range_B_refined 11.042 r_dihedral_angle_2_deg 9.768 r_scangle_other 7.787 r_dihedral_angle_1_deg 7.03 r_mcangle_other 5.042 r_mcangle_it 5.04 r_scbond_it 4.969 r_scbond_other 4.967
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.481 r_long_range_B_other 11.048 r_long_range_B_refined 11.042 r_dihedral_angle_2_deg 9.768 r_scangle_other 7.787 r_dihedral_angle_1_deg 7.03 r_mcangle_other 5.042 r_mcangle_it 5.04 r_scbond_it 4.969 r_scbond_other 4.967 r_mcbond_it 3.341 r_mcbond_other 3.332 r_angle_refined_deg 1.659 r_angle_other_deg 0.567 r_chiral_restr 0.081 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 3084 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 168
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction