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Autonomous VH domain that interacts with eIF4E at the Capped mRNA Binding site.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BEA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M TRIS.HCl pH 8.5 25% (v/v) PEG 550 MME
Crystal Properties Matthews coefficient Solvent content 2.19 43.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.522 α = 90 b = 81.819 β = 90 c = 122.987 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 9M 2018-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95372 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.25 40.996 100 0.12 4.7 13.4 19226
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.37 100 0.755 1 12.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4BEA 2.25 40.943 19171 976 99.969 0.217 0.2145 0.2201 0.266 0.2734 48.131
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] -2.942 8.55 -5.608
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.574 r_dihedral_angle_3_deg 17.256 r_dihedral_angle_4_deg 15.616 r_dihedral_angle_1_deg 7.437 r_lrange_it 7.098 r_lrange_other 7.091 r_scangle_it 5.01 r_scangle_other 5.01 r_mcangle_it 4.452 r_mcangle_other 4.451
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.574 r_dihedral_angle_3_deg 17.256 r_dihedral_angle_4_deg 15.616 r_dihedral_angle_1_deg 7.437 r_lrange_it 7.098 r_lrange_other 7.091 r_scangle_it 5.01 r_scangle_other 5.01 r_mcangle_it 4.452 r_mcangle_other 4.451 r_scbond_it 3.011 r_scbond_other 3.01 r_mcbond_it 2.86 r_mcbond_other 2.858 r_angle_refined_deg 1.311 r_angle_other_deg 1.165 r_symmetry_nbd_refined 0.238 r_nbd_other 0.227 r_symmetry_nbd_other 0.182 r_nbd_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.176 r_nbtor_refined 0.161 r_xyhbond_nbd_refined 0.158 r_symmetry_nbtor_other 0.075 r_symmetry_xyhbond_nbd_other 0.055 r_chiral_restr 0.051 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2490 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing