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Structural Analysis of Leishmania mexicana eukaryotic initiation factor 5a
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, SITTING DROP 5 277 PEG 8000,Ammonium phosphate-monobasic, Sodium Acetate , pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.9 57.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.205 α = 90 b = 65.205 β = 90 c = 89.435 γ = 120
Symmetry Space Group P 32 2 1
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 2004-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9791 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.7 20 98.4 0.14 6.2 3.6 6232 6232 -3 64.39
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.85 98.8 0.501 2.4 3.3 885
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 pdb entry 1x6o 2.7 20 5939 5939 291 98.8 0.22462 0.22462 0.22054 0.2252 0.30183 0.3049 RANDOM 37.328
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] 0.29 0.15 0.29 -0.44
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 7.702 r_dihedral_angle_1_deg 6.999 r_scbond_it 5.625 r_mcangle_it 3.959 r_mcbond_it 2.509 r_angle_refined_deg 1.666 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.203 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.106
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 7.702 r_dihedral_angle_1_deg 6.999 r_scbond_it 5.625 r_mcangle_it 3.959 r_mcbond_it 2.509 r_angle_refined_deg 1.666 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.203 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.106 r_symmetry_hbond_refined 0.075 r_bond_refined_d 0.02 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_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 1118 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing