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The crystal structure of iron superoxide dismutase from Aliivibrio salmonicida.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ISA PDB ENTRY 1ISA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 1 MICROLITER DROPS OF A 6.5 MG/ML PROTEIN SOLUTION WITH A SOLUTION CONTAINING 0.1M TRIS-HCL, 1.4 M SODIUM CITRATE, PH 8.5 AT 291K.
Crystal Properties Matthews coefficient Solvent content 2.87 57.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.72 α = 90 b = 70.72 β = 90 c = 170.25 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 110 IMAGE PLATE MARRESEARCH 2006-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM1A ESRF BM1A
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 1.7 50 99.8 0.12 9.5 5.8 55155 15.51
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 1.7 1.79 98.6 0.34 3.6 5.5
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 1ISA 1.7 15 52997 1984 99.8 0.207 0.205 0.2087 0.239 0.2406 RANDOM 21
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] 0.91 0.45 0.91 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.352 r_dihedral_angle_3_deg 13.988 r_dihedral_angle_4_deg 9.829 r_dihedral_angle_1_deg 5.82 r_scangle_it 3.046 r_scbond_it 2.127 r_angle_refined_deg 1.467 r_mcangle_it 1.431 r_mcbond_it 0.858 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.352 r_dihedral_angle_3_deg 13.988 r_dihedral_angle_4_deg 9.829 r_dihedral_angle_1_deg 5.82 r_scangle_it 3.046 r_scbond_it 2.127 r_angle_refined_deg 1.467 r_mcangle_it 1.431 r_mcbond_it 0.858 r_nbtor_refined 0.314 r_symmetry_hbond_refined 0.246 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.166 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.105 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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_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 3018 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing