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Crystal structure of human eukaryotic translation initiation factor EIF5A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X6O PDB entry 1X6O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 22% PEG 3350, 0.2M Ammonium sulfate, 0.1M Sodium cacodylate. Cryoprotected with 20% PEG 3350 and 20% Ethylene glycol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.57 52.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.119 α = 90 b = 76.119 β = 90 c = 107.752 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 IMAGE PLATE RIGAKU RAXIS 2008-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.5418
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 2.5 20 100 0.076 14.3 12.7 11503
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 2.5 2.59 100 0.964 12.8 1123
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1X6O 2.5 19.996 11434 521 99.712 0.246 0.244 0.2821 0.3 0.3244 Thin shells 36.775
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] 1.07 1.07 -2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.229 r_dihedral_angle_4_deg 18.698 r_dihedral_angle_3_deg 16.118 r_dihedral_angle_1_deg 6.078 r_mcangle_it 1.586 r_scangle_it 1.564 r_angle_other_deg 1.349 r_angle_refined_deg 1.338 r_scbond_it 1.018 r_mcbond_it 0.954
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.229 r_dihedral_angle_4_deg 18.698 r_dihedral_angle_3_deg 16.118 r_dihedral_angle_1_deg 6.078 r_mcangle_it 1.586 r_scangle_it 1.564 r_angle_other_deg 1.349 r_angle_refined_deg 1.338 r_scbond_it 1.018 r_mcbond_it 0.954 r_mcbond_other 0.186 r_chiral_restr 0.064 r_bond_refined_d 0.014 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 1889 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 6
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction