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Crystal structure of the human eIF4E-4EBP1 peptide complex without cap
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IPB PDB ENTRY 1IPB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 1:1 of (protein stock: 0.0004 M eif4e, 0.001 M 4epb1, 0.004 M ribavirin, 0.02 HEPES, 0.1 M potassium chloride, 0.001 tcep, ph 7.3):(reservoir: 2 M ammonium sulfate, 2% Peg-400, 0.1 M sodium HEPES), vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.79 55.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.5 α = 90 b = 38.263 β = 97.97 c = 93.533 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 100 CCD ADSC QUANTUM 315 2010-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97924 APS 19-ID
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 2.1 50 99.7 0.089 7.6 3.6 35859
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 2.1 2.14 96.9 0.64 3.4 1728
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 1IPB 2.1 30 35692 1503 98.947 0.199 0.1982 0.209 0.2239 0.2327 THIN SHELLS (SFTOOLS) 41.169
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] 0.746 2.148 -0.441 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.033 r_dihedral_angle_4_deg 17.783 r_dihedral_angle_3_deg 12.499 r_dihedral_angle_1_deg 6.494 r_scangle_it 3.024 r_scbond_it 1.902 r_angle_refined_deg 1.316 r_mcangle_it 1.257 r_angle_other_deg 0.894 r_mcbond_it 0.688
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.033 r_dihedral_angle_4_deg 17.783 r_dihedral_angle_3_deg 12.499 r_dihedral_angle_1_deg 6.494 r_scangle_it 3.024 r_scbond_it 1.902 r_angle_refined_deg 1.316 r_mcangle_it 1.257 r_angle_other_deg 0.894 r_mcbond_it 0.688 r_mcbond_other 0.147 r_chiral_restr 0.08 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3205 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 40
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling