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Crystal structure of a putative iron superoxide dismutase from Trypanosoma cruzi bound to iron
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F2N PDB ENTRY 4F2N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 TrcrA.00198.b.B1 PS01521 at 23.05 mg/mL against JCSG+ screen condition G1: 0.1 M HEPES, pH 7.0, 30% Jeffamine ED-2001, crystal tracking ID 235439g1, unique puck ID gvr7-6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.94 36.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.65 α = 90 b = 75.68 β = 90 c = 117.45 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 CCD RIGAKU SATURN 944+ VariMax 2012-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 2.25 50 97 0.137 13.4 7.2 20854 20226 -3 19.81
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 2.25 2.31 94.4 0.37 5.99
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 4F2N 2.25 44.19 19189 1038 96.98 0.173 0.1709 0.1786 0.2122 0.2161 RANDOM 13.3107
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] -0.54 0.19 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.245 r_dihedral_angle_3_deg 12.935 r_dihedral_angle_4_deg 11.965 r_dihedral_angle_1_deg 6.073 r_angle_refined_deg 1.407 r_angle_other_deg 1.008 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.245 r_dihedral_angle_3_deg 12.935 r_dihedral_angle_4_deg 11.965 r_dihedral_angle_1_deg 6.073 r_angle_refined_deg 1.407 r_angle_other_deg 1.008 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3350 Nucleic Acid Atoms Solvent Atoms 348 Heterogen Atoms 2
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction