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The 1.6 A Structure of Fe-Superoxide Dismutase from the thermophilic cyanobacterium Thermosynechococcus elongatus : Correlation of EPR and Structural Characteristics
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ISC FeSOD from E.coli, PDB entry 1isc
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 293.15 VAPOR DIFFUSION, HANGING DROP, 293.15K, 0.1M Sodium Cacodylate pH 6.7, 0.2M Magnesium Acetate Tetrahydrate, 20% PEG 6K
Crystal Properties Matthews coefficient Solvent content 2.61 52.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.749 α = 90 b = 63.644 β = 110.45 c = 74.709 γ = 90
Symmetry Space Group P 1 21 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 4 2002-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 1.100 NSLS X8C
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 1.6 70 94.5 0.088 6.35 16.18 53851 -3 15.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.642 93.4 0.32 0.32 6.35 14.28 5643
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT FeSOD from E.coli, PDB entry 1isc 1.6 70 53851 2896 94.46 0.19577 0.19377 0.23208 0.27 RANDOM 15.669
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] 1.64 0.82 -1.54 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.88 r_scangle_it 3.693 r_sphericity_free 3.671 r_scbond_it 2.616 r_sphericity_bonded 2.124 r_mcangle_it 1.91 r_angle_refined_deg 1.623 r_rigid_bond_restr 1.522 r_mcbond_it 1.312 r_angle_other_deg 0.903
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.88 r_scangle_it 3.693 r_sphericity_free 3.671 r_scbond_it 2.616 r_sphericity_bonded 2.124 r_mcangle_it 1.91 r_angle_refined_deg 1.623 r_rigid_bond_restr 1.522 r_mcbond_it 1.312 r_angle_other_deg 0.903 r_symmetry_vdw_other 0.297 r_nbd_other 0.247 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.213 r_symmetry_hbond_refined 0.206 r_symmetry_vdw_refined 0.177 r_chiral_restr 0.107 r_nbtor_other 0.087 r_bond_refined_d 0.016 r_gen_planes_other 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_xyhbond_nbd_other r_symmetry_hbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3128 Nucleic Acid Atoms Solvent Atoms 565 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement EPMR phasing