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Crystal Structure of eIF4E in Complex with a Stapled Peptide Derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AZA PDB ENTRY 4AZA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 18-26% OF POLYETHYLENE GLYCOL 3350, 0.01-02M AMMONIUM SULPHATE AND 100MM BIS-TRIS AT PH 5.5
Crystal Properties Matthews coefficient Solvent content 2.42 49.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.301 α = 90 b = 91.677 β = 90 c = 137.908 γ = 90
Symmetry Space Group C 2 2 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 CCD MIRRORS 2012-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER X8 PROTEUM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.57 68.95 98.8 0.09 11.08 10.15 8036 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.57 2.63 83.2 0.46 2.33 2.64
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 4AZA 2.57 45.88 7640 371 98.88 0.22232 0.22025 0.2254 0.26575 0.2623 RANDOM 15.144
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] -0.36 0.4 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.071 r_dihedral_angle_4_deg 19.858 r_dihedral_angle_3_deg 16.827 r_dihedral_angle_1_deg 6.932 r_angle_refined_deg 1.355 r_angle_other_deg 0.781 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.071 r_dihedral_angle_4_deg 19.858 r_dihedral_angle_3_deg 16.827 r_dihedral_angle_1_deg 6.932 r_angle_refined_deg 1.355 r_angle_other_deg 0.781 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.001 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1601 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PROTEUM2 data reduction PROTEUM2 data scaling PHASER phasing