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Crystal structure of eIF4e in complex with Compound 5-PA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TQC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 26% Peg 3350, 0.1 M MES pH 6.0, 10% isopropanol and 2 mM CaCl2
Crystal Properties Matthews coefficient Solvent content 2.14 42.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.194 α = 90 b = 74.397 β = 97.38 c = 52.454 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 PIXEL DECTRIS EIGER X 9M 2022-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.1271 APS 21-ID-D
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 2.091 50 98 0.102 0.114 0.049 1 9.1 5.6 21714
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 2.1 2.14 95.8 0.316 0.353 0.154 0.91 5.2
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 (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 2.091 33.5 21660 1050 97.3 0.2005 0.1982 0.1935 0.247 0.2376 RANDOM 27.91
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] 2.9194 -1.9081 0.1162 -3.0356
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.41 t_omega_torsion 3.23 t_angle_deg 0.88 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.41 t_omega_torsion 3.23 t_angle_deg 0.88 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2986 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 64
Software Software Software Name Purpose BUSTER refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing