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Crystal structure of the human eIF4A1/AMPPNP/amidino-rocaglate/polypurine RNA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZC9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 290 0.2 M ammonium acetate, 8% PEG20000, 10% Hampton Silver Bullet Reagent B5 (0.33% w/v 2,7-naphthalenedisulfonic acid disodium salt, 0.33% w/v azelaic acid, 0.33% w/v trans-cinnamic acid, 0.02 M HEPES sodium pH 6.8)
Crystal Properties Matthews coefficient Solvent content 2.54 51.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.11 α = 95.22 b = 87.314 β = 105.29 c = 93.159 γ = 108.35
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 EIGER X 9M 2023-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.920105 NSLS-II 17-ID-1
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 1.689 81.362 96 0.09 0.11 0.061 0.993 5.61 3 201775
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 1.69 1.75 91.16 1.18 1.45 0.84 0.368 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.69 40.68 1.96 201757 1999 95.99 0.2033 0.2029 0.2034 0.2402 0.2404 40.02
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.609 f_angle_d 1.2678 f_chiral_restr 0.0674 f_plane_restr 0.0193 f_bond_d 0.0122
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12035 Nucleic Acid Atoms 720 Solvent Atoms 899 Heterogen Atoms 292
Software Software Software Name Purpose autoPROC data processing PHENIX phasing PHENIX model building PHENIX refinement