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The crystal structure of the enzyme Fe-superoxide dismutase from Plasmodium falciparum
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 25.5% PEG 4000 (w/v), 0.17 M Sodium Acetate, 0.085 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.12 41.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.402 α = 90 b = 78.417 β = 90 c = 88.369 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 RIGAKU RAXIS IIC 2002-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 31.62 95.3 0.098 7.5 6.4 25131 2 2
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 2.11 73.3 0.37 2 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 2 31.62 2 24057 24057 1266 94.97 0.15769 0.15576 0.1692 0.19389 0.172 RANDOM 14.498
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.576 r_scangle_it 2.525 r_scbond_it 1.558 r_angle_refined_deg 1.107 r_mcangle_it 1.053 r_angle_other_deg 0.796 r_mcbond_it 0.55 r_symmetry_vdw_other 0.273 r_nbd_other 0.232 r_symmetry_hbond_refined 0.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.576 r_scangle_it 2.525 r_scbond_it 1.558 r_angle_refined_deg 1.107 r_mcangle_it 1.053 r_angle_other_deg 0.796 r_mcbond_it 0.55 r_symmetry_vdw_other 0.273 r_nbd_other 0.232 r_symmetry_hbond_refined 0.216 r_nbd_refined 0.195 r_xyhbond_nbd_refined 0.143 r_symmetry_vdw_refined 0.135 r_nbtor_other 0.084 r_chiral_restr 0.072 r_metal_ion_refined 0.04 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3175 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement