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Structure of the DEAD domain of Human eukaryotic initiation factor 4A, eIF4A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QDE pdb entry 1QDE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 20% PEG3350, 200 mM Ammonium Nitrate, 500 mM NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.14 42.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.799 α = 90 b = 78.252 β = 103.43 c = 59.088 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 CCD ADSC QUANTUM 4 2006-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.93300 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.25 20 99.65 0.071 7.4 3.45 19100 19100 25.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.25 2.37 100 0.241 5.3 3.46 2912
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1QDE 2.25 20 19100 19100 1026 99.65 0.18026 0.18026 0.1761 0.1905 0.2573 0.2635 RANDOM 14.89
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] -0.58 -0.56 1.49 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.063 r_dihedral_angle_4_deg 16.623 r_dihedral_angle_3_deg 16.301 r_dihedral_angle_1_deg 8.03 r_scangle_it 3.812 r_scbond_it 2.433 r_angle_refined_deg 1.732 r_mcangle_it 1.384 r_mcbond_it 0.912 r_symmetry_hbond_refined 0.341
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.063 r_dihedral_angle_4_deg 16.623 r_dihedral_angle_3_deg 16.301 r_dihedral_angle_1_deg 8.03 r_scangle_it 3.812 r_scbond_it 2.433 r_angle_refined_deg 1.732 r_mcangle_it 1.384 r_mcbond_it 0.912 r_symmetry_hbond_refined 0.341 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.3 r_nbd_refined 0.235 r_xyhbond_nbd_refined 0.182 r_chiral_restr 0.127 r_bond_refined_d 0.018 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3431 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing