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Crystal Structure of the C-terminal Domain of Human eIF2D at 1.4 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 3.5 M Sodium Formate, 100 mM Sodium Acetate pH4.5
Crystal Properties Matthews coefficient Solvent content 2.59 52.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.65 α = 90 b = 50.65 β = 90 c = 183.653 γ = 90
Symmetry Space Group P 43 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 PILATUS 6M-F 2016-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1.00 APS 24-ID-C
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 1.4 48.83 99.1 0.043 0.049 0.023 0.999 14.7 4.2 47791
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 1.4 1.42 94.2 1.098 1.297 0.674 0.5 3.1
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 SAD THROUGHOUT 1.4 48.83 45498 2259 98.65 0.1419 0.1404 0.1407 0.1718 0.1703 RANDOM 29.529
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] 0.37 0.37 -0.73
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 40.095 r_dihedral_angle_2_deg 37.651 r_sphericity_bonded 14.981 r_dihedral_angle_4_deg 12.333 r_dihedral_angle_3_deg 10.966 r_dihedral_angle_1_deg 4.952 r_rigid_bond_restr 1.506 r_angle_refined_deg 1.346 r_angle_other_deg 0.913 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 40.095 r_dihedral_angle_2_deg 37.651 r_sphericity_bonded 14.981 r_dihedral_angle_4_deg 12.333 r_dihedral_angle_3_deg 10.966 r_dihedral_angle_1_deg 4.952 r_rigid_bond_restr 1.506 r_angle_refined_deg 1.346 r_angle_other_deg 0.913 r_chiral_restr 0.089 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1581 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction SHELX data reduction SHELXDE phasing