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Crystal structure of human eIF2 alpha-gamma complexed with PPP1R15A_420-452
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AlphaFold2-multimer
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 11-12% PEG 6000, 0.1M Tris-HCl pH8.5 supplemented with amino acids
Crystal Properties Matthews coefficient Solvent content 3.25 62.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.594 α = 90 b = 120.594 β = 90 c = 158.259 γ = 90
Symmetry Space Group P 41 21 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 9M 2023-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.6199 Diamond I24
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 3.35 41.17 99.9 0.271 0.28 0.113 0.996 7.2 12.3 17421
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 3.35 3.62 2.618 2.714 1.109 0.521
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 3.35 41.15 16510 859 99.9 0.24368 0.2407 0.2419 0.29915 0.2997 RANDOM 140.91
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] -5.41 -5.41 10.82
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 40.725 r_long_range_B_other 40.724 r_scangle_other 35.417 r_mcangle_it 31.57 r_mcangle_other 31.567 r_scbond_it 24.686 r_scbond_other 24.617 r_mcbond_it 22.442 r_mcbond_other 22.44 r_dihedral_angle_3_deg 15.356
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 40.725 r_long_range_B_other 40.724 r_scangle_other 35.417 r_mcangle_it 31.57 r_mcangle_other 31.567 r_scbond_it 24.686 r_scbond_other 24.617 r_mcbond_it 22.442 r_mcbond_other 22.44 r_dihedral_angle_3_deg 15.356 r_dihedral_angle_1_deg 8.729 r_dihedral_angle_2_deg 6.324 r_angle_refined_deg 1.911 r_angle_other_deg 0.607 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4218 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing