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Crystal structure analysis of eukaryotic translation initiation factor 5B structure I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.2M Tri-Sodium Citrate, 19% PEG 3350, HEPES pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.57 α = 90 b = 129.57 β = 90 c = 70.51 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 CCD ADSC QUANTUM 315 2008-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU
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 2.35 43.19 99.6 0.091 22.79 14.1 25590 -3 54.799
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.49 97.6 0.997 1.034 3.19
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 2.35 40.97 25589 1821 99.56 0.2145 0.2104 0.2012 0.2677 0.2529 RANDOM 53.8743
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] -0.09 -0.09 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.953 r_dihedral_angle_3_deg 14.337 r_dihedral_angle_4_deg 13.728 r_dihedral_angle_1_deg 5.569 r_mcangle_it 4.924 r_scbond_it 3.938 r_mcbond_it 3.101 r_angle_refined_deg 1.113 r_chiral_restr 0.07 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.953 r_dihedral_angle_3_deg 14.337 r_dihedral_angle_4_deg 13.728 r_dihedral_angle_1_deg 5.569 r_mcangle_it 4.924 r_scbond_it 3.938 r_mcbond_it 3.101 r_angle_refined_deg 1.113 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4614 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SHELXCD phasing SOLVE phasing RESOLVE phasing