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Crystal structure of human Eukaryotic translation initiation factor 2A (eIF2A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WJ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 30% PEG 2K, 0.2M Potassium Bromide
Crystal Properties Matthews coefficient Solvent content 1.7 27.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.289 α = 90 b = 84.847 β = 90 c = 99.34 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS EIGER X 16M 2020-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
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 1.8 47.68 98.8 0.108 0.117 0.043 0.995 13.5 7.7 42642
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 1.8 1.84 98.1 0.808 0.864 0.304 0.832 7.9
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 3WJ9 1.8 47.68 40514 2087 98.46 0.2009 0.1995 0.207 0.2276 0.2319 RANDOM 25.797
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] 1.38 -0.7 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.418 r_dihedral_angle_4_deg 22.738 r_dihedral_angle_3_deg 12.038 r_dihedral_angle_1_deg 8.119 r_angle_refined_deg 1.436 r_angle_other_deg 1.356 r_chiral_restr 0.06 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.418 r_dihedral_angle_4_deg 22.738 r_dihedral_angle_3_deg 12.038 r_dihedral_angle_1_deg 8.119 r_angle_refined_deg 1.436 r_angle_other_deg 1.356 r_chiral_restr 0.06 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3157 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 17
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction