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The crystal structure of the eukaryotic FeSOD from Vigna unguiculata suggests a new enzymatic mechanism
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DT0 PDB ENTRY 1DT0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 200 MM AMMONIUM SULFATE, 100 MM SODIUM ACETATE PH 5.0, 25%(W/V) POLYETHYLENE GLYCOL 4000
Crystal Properties Matthews coefficient Solvent content 2.23 44.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.985 α = 90 b = 48.163 β = 119.76 c = 63.671 γ = 90
Symmetry Space Group C 1 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 MARRESEARCH 2002-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 1.8 30 99 0.1 6.2 3.3 20443 2
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 1.8 1.9 99 0.77 0.9 3.1
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 1DT0 1.97 28.77 14661 772 99.6 0.15 0.148 0.1555 0.192 0.1986 RANDOM 22.65
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] -0.03 0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.375 r_dihedral_angle_3_deg 16.262 r_dihedral_angle_4_deg 12.073 r_dihedral_angle_1_deg 7.764 r_scangle_it 3.441 r_mcangle_it 3.38 r_scbond_it 2.434 r_mcbond_it 2.281 r_angle_refined_deg 1.585 r_symmetry_hbond_refined 0.362
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.375 r_dihedral_angle_3_deg 16.262 r_dihedral_angle_4_deg 12.073 r_dihedral_angle_1_deg 7.764 r_scangle_it 3.441 r_mcangle_it 3.38 r_scbond_it 2.434 r_mcbond_it 2.281 r_angle_refined_deg 1.585 r_symmetry_hbond_refined 0.362 r_nbtor_refined 0.323 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.205 r_symmetry_vdw_refined 0.192 r_chiral_restr 0.19 r_metal_ion_refined 0.076 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1724 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling EPMR phasing