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Crystal Structure of De Novo Protein Inhibitor of eEF2K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 60 % tacsimate
Crystal Properties Matthews coefficient Solvent content 2.79 55.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.97 α = 90 b = 86.97 β = 90 c = 221.58 γ = 120
Symmetry Space Group P 65 2 2
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 EIGER2 X 16M 2025-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.49 44.63 99.5 0.83 14.7 4.1 18127
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 2.492 44.625 18127 882 99.972 0.202 0.1988 0.1988 0.2759 0.2762 48.021
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] 0.225 0.112 0.225 -0.729
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 30.523 r_lrange_it 30.52 r_scangle_it 29.474 r_scangle_other 29.468 r_scbond_it 22.207 r_scbond_other 22.201 r_mcangle_it 20.857 r_mcangle_other 20.854 r_dihedral_angle_3_deg 20.519 r_dihedral_angle_2_deg 17.506
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 30.523 r_lrange_it 30.52 r_scangle_it 29.474 r_scangle_other 29.468 r_scbond_it 22.207 r_scbond_other 22.201 r_mcangle_it 20.857 r_mcangle_other 20.854 r_dihedral_angle_3_deg 20.519 r_dihedral_angle_2_deg 17.506 r_mcbond_it 16.509 r_mcbond_other 16.49 r_dihedral_angle_6_deg 15.859 r_dihedral_angle_1_deg 9.184 r_angle_refined_deg 3.99 r_angle_other_deg 1.409 r_symmetry_nbd_refined 0.356 r_xyhbond_nbd_refined 0.307 r_symmetry_xyhbond_nbd_refined 0.262 r_nbd_refined 0.26 r_nbd_other 0.228 r_chiral_restr 0.211 r_nbtor_refined 0.189 r_symmetry_nbd_other 0.18 r_symmetry_xyhbond_nbd_other 0.142 r_symmetry_nbtor_other 0.102 r_metal_ion_refined 0.059 r_bond_refined_d 0.027 r_gen_planes_refined 0.016 r_ext_dist_refined_b 0.004 r_gen_planes_other 0.004 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3012 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing