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Crystal structure of eukaryotic translation initiation factor eIF-5A2 from Arabidopsis thaliana
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 7.5 289 25% ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.95 58.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.56 α = 90 b = 79.83 β = 90 c = 94.95 γ = 90
Symmetry Space Group P 21 21 21
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 MAR scanner 345 mm plate 2005-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 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 2.23 94.92 99.5 0.066 20393
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.23 2.28
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 2.3 94.92 18539 1183 99.78 0.20435 0.20201 0.1977 0.24074 0.2328 RANDOM 21.554
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] -1.21 1.66 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.2 r_dihedral_angle_4_deg 22.012 r_dihedral_angle_3_deg 15.588 r_dihedral_angle_1_deg 6.245 r_scangle_it 3.533 r_scbond_it 2.127 r_mcangle_it 1.315 r_angle_refined_deg 1.266 r_mcbond_it 1.224 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.2 r_dihedral_angle_4_deg 22.012 r_dihedral_angle_3_deg 15.588 r_dihedral_angle_1_deg 6.245 r_scangle_it 3.533 r_scbond_it 2.127 r_mcangle_it 1.315 r_angle_refined_deg 1.266 r_mcbond_it 1.224 r_nbtor_refined 0.293 r_symmetry_hbond_refined 0.221 r_symmetry_vdw_refined 0.202 r_nbd_refined 0.194 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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 2163 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 24
Software Software Software Name Purpose MAR345dtb data collection PHASES phasing REFMAC refinement MOSFLM data reduction SCALA data scaling