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Crystal structure of Trypanosoma cruzi mitochondrial iron superoxide dismutase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NYB PDB ENTRY 2NYB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 291 30% PEG 4000, 0.1M Tris.HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.1 41.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.17 α = 90 b = 74.55 β = 96.81 c = 56.85 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 2011-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 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 2.23 39.64 93.1 0.096 13.4 6.5 18138 18138
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 2.21 2.33 73.6 0.351 0.351 2.1 5.8
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2NYB 2.23 24.17 18121 1368 98.6 0.172 0.168 0.1695 0.22 0.2184 28.56
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] 7.3967 0.3815 -9.129 1.7322
RMS Deviations Key Refinement Restraint Deviation t_angle_deg 1.09 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_omega_torsion
RMS Deviations Key Refinement Restraint Deviation t_angle_deg 1.09 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_omega_torsion t_other_torsion t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3227 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 2
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection BUSTER refinement