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Crystal Structure of the enzyme Fe-superoxide dismutase TbSODB2 from Trypanosoma brucei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GPC PDB entry 2GPC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 8.5 291 0.1 M Tris pH 8.5, 24-30% PEG4000 and 0.2 M MgCl2, hanging drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.27 45.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.302 α = 90 b = 76.504 β = 92.7 c = 76.981 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 IMAGE PLATE MAR scanner 345 mm plate 2006-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 30.3 98.4 0.08 0.08 4.4 52771 52751 2 2
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 2 2.059 89.7 0.298 0.298 3.8 2.9
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 (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 2GPC 2.01 30.18 50082 50085 2666 99.44 0.17721 0.17499 0.1758 0.21911 0.2198 RANDOM 20.698
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] -0.02 -0.01 0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.749 r_dihedral_angle_3_deg 14.873 r_dihedral_angle_4_deg 14.124 r_dihedral_angle_1_deg 10.312 r_scangle_it 2.686 r_scbond_it 1.753 r_angle_refined_deg 1.418 r_mcangle_it 0.881 r_mcbond_it 0.564 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.749 r_dihedral_angle_3_deg 14.873 r_dihedral_angle_4_deg 14.124 r_dihedral_angle_1_deg 10.312 r_scangle_it 2.686 r_scbond_it 1.753 r_angle_refined_deg 1.418 r_mcangle_it 0.881 r_mcbond_it 0.564 r_nbtor_refined 0.302 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.192 r_xyhbond_nbd_refined 0.157 r_symmetry_hbond_refined 0.144 r_chiral_restr 0.103 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_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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6272 Nucleic Acid Atoms Solvent Atoms 706 Heterogen Atoms 4
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection