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eIF4E in Complex with a Disulphide-Free Autonomous VH Domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V8W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 289 25% (w/v) PEG 6000, 0.01-02 M Ammonium Sulphate, 100mM Tris, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.26 45.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 198.848 α = 90 b = 45.324 β = 93.192 c = 39.763 γ = 90
Symmetry Space Group C 1 2 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 2018-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.953700 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 1.668 44.229 99.4 0.116 6.1 3.7 41261 3.3
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 1.67 1.76 0.673 1.1
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 2V8W 1.668 44.226 41261 2061 99.441 0.183 0.1815 0.1924 0.2064 0.2146 12.212
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] 0.47 -0.241 0.051 -0.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.413 r_dihedral_angle_4_deg 15.256 r_dihedral_angle_3_deg 11.016 r_dihedral_angle_1_deg 7.082 r_lrange_it 4.241 r_lrange_other 4.24 r_scangle_it 1.348 r_scangle_other 1.348 r_angle_other_deg 1.261 r_mcangle_it 1.241
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.413 r_dihedral_angle_4_deg 15.256 r_dihedral_angle_3_deg 11.016 r_dihedral_angle_1_deg 7.082 r_lrange_it 4.241 r_lrange_other 4.24 r_scangle_it 1.348 r_scangle_other 1.348 r_angle_other_deg 1.261 r_mcangle_it 1.241 r_mcangle_other 1.232 r_angle_refined_deg 1.197 r_scbond_it 0.786 r_scbond_other 0.786 r_mcbond_it 0.695 r_mcbond_other 0.681 r_nbd_other 0.228 r_nbd_refined 0.182 r_symmetry_nbd_other 0.174 r_symmetry_nbd_refined 0.163 r_nbtor_refined 0.161 r_xyhbond_nbd_refined 0.147 r_symmetry_xyhbond_nbd_refined 0.137 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.052 r_bond_refined_d 0.004 r_gen_planes_refined 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 2484 Nucleic Acid Atoms Solvent Atoms 408 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing