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Crystal structure of the full length eIF5A from Saccharomyces cerevisiae
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 6.5 291 0.1M MES, 30% PEG400, 0.1M MgCl2, 3% Glicerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.37 48.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.664 α = 90 b = 59.664 β = 90 c = 339.79 γ = 120
Symmetry Space Group P 65 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 MAR CCD 165 mm 2006-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.427 LNLS D03B-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 3.35 49.45 92.1 0.082 5.6 5431
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) 3.35 3.53 89.5 0.46 2.6 6
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 3.35 49.45 4815 528 91.93 0.3916 0.38555 0.3813 0.44824 0.4452 RANDOM 84.487
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] 0.59 0.29 0.59 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.068 r_dihedral_angle_3_deg 22.226 r_dihedral_angle_1_deg 22.006 r_dihedral_angle_4_deg 17.864 r_angle_refined_deg 2.149 r_scangle_it 0.457 r_symmetry_hbond_refined 0.421 r_symmetry_vdw_refined 0.323 r_nbtor_refined 0.313 r_nbd_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.068 r_dihedral_angle_3_deg 22.226 r_dihedral_angle_1_deg 22.006 r_dihedral_angle_4_deg 17.864 r_angle_refined_deg 2.149 r_scangle_it 0.457 r_symmetry_hbond_refined 0.421 r_symmetry_vdw_refined 0.323 r_nbtor_refined 0.313 r_nbd_refined 0.297 r_scbond_it 0.287 r_mcangle_it 0.229 r_xyhbond_nbd_refined 0.22 r_chiral_restr 0.169 r_mcbond_it 0.135 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2105 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling