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Crystal structure of apoform human eIF4A1 C-terminal domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZU6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 18.5% (w/v) PEG 8000, 0.2M sodium acetate trihydrate, 0.1M MES, pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.43 49.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.97 α = 90 b = 84.97 β = 90 c = 66.42 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2018-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.73 42.49 100 0.189 0.994 8.2 6.4 14242
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.73 2.78 1.375 0.507
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.731 40.003 14224 674 99.86 0.232 0.2287 0.2323 0.2937 0.2936 62.688
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] 1.372 0.686 1.372 -4.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.199 r_dihedral_angle_6_deg 14.34 r_dihedral_angle_1_deg 7.72 r_lrange_it 7.015 r_lrange_other 7.014 r_dihedral_angle_2_deg 5.35 r_mcangle_it 4.833 r_mcangle_other 4.832 r_scangle_it 4.783 r_scangle_other 4.782
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.199 r_dihedral_angle_6_deg 14.34 r_dihedral_angle_1_deg 7.72 r_lrange_it 7.015 r_lrange_other 7.014 r_dihedral_angle_2_deg 5.35 r_mcangle_it 4.833 r_mcangle_other 4.832 r_scangle_it 4.783 r_scangle_other 4.782 r_mcbond_it 2.966 r_mcbond_other 2.966 r_scbond_it 2.91 r_scbond_other 2.909 r_angle_refined_deg 1.438 r_angle_other_deg 0.523 r_symmetry_nbd_refined 0.306 r_symmetry_xyhbond_nbd_refined 0.291 r_nbd_refined 0.241 r_symmetry_nbd_other 0.213 r_nbd_other 0.202 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.152 r_ncsr_local_group_1 0.137 r_ncsr_local_group_2 0.109 r_ncsr_local_group_3 0.09 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.07 r_xyhbond_nbd_other 0.062 r_bond_refined_d 0.006 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 3732 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing