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Leishmania IF4E-1 bound to Leishmania 4E-IP1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WKW TRUNCATED VERSION OF AN EIF4E, M7GTP, 4E-BP1 COMPLEX WITH PDB ID 1WKW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 298 0.1 M Tris-HCl
3 % polyethylene glycol 400
2.125-2.175 M of ammonium sulfate.
Crystal Properties Matthews coefficient Solvent content 2.49 50.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.22 α = 90 b = 68.22 β = 90 c = 220.2 γ = 120
Symmetry Space Group P 62 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 CCD ADSC QUANTUM 315r 2013-04-19 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315r 2013-04-19 M SINGLE WAVELENGTH 3 1 x-ray 100 CCD ADSC QUANTUM 315r 2013-04-19 M SINGLE WAVELENGTH 4 1 x-ray 100 CCD ADSC QUANTUM 315r 2013-04-19 M SINGLE WAVELENGTH 5 1 x-ray 100 CCD ADSC QUANTUM 315r 2013-04-19 M SINGLE WAVELENGTH 6 1 x-ray 100 CCD ADSC QUANTUM 315r 2013-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.999909 ALS 8.2.2 2 SYNCHROTRON ALS BEAMLINE 8.2.2 0.999925 ALS 8.2.2 3 SYNCHROTRON ALS BEAMLINE 8.2.2 0.999893 ALS 8.2.2 4 SYNCHROTRON ALS BEAMLINE 8.2.2 0.999887 ALS 8.2.2 5 SYNCHROTRON ALS BEAMLINE 8.2.2 0.999925 ALS 8.2.2 6 SYNCHROTRON ALS BEAMLINE 8.2.2 0.999887 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.7 36.7 99.8 0.133 0.134 0.999 37.1 64.813 9019
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.77 100 0.474 0.477 0.996 14.68 70.79
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT TRUNCATED VERSION OF AN EIF4E, M7GTP, 4E-BP1 COMPLEX WITH PDB ID 1WKW 2.7 36.7 1.35 9015 439 99.83 0.2421 0.24 0.2422 0.2827 0.2895 66.2755
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.935 f_angle_d 0.484 f_chiral_restr 0.041 f_bond_d 0.003 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1650 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 17
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PDB_EXTRACT data extraction TRUNCATE data reduction PHASER phasing