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Crystal structure of human mitochondrial ferritin (hMTF) Fe(II)-loaded for 60 minutes showing either a dioxygen or a superoxide anion coordinated to iron ions in the ferroxidase site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R03
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 281.15 1.6-2 M MgCl2 6H2O and 0.1 M bicine pH 9.0
Crystal Properties Matthews coefficient Solvent content 3.18 61.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.83 α = 90 b = 183.83 β = 90 c = 183.83 γ = 90
Symmetry Space Group F 4 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2018-02-19 M MAD 2 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2018-02-19 M MAD 3 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2018-02-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97622 Diamond I03 2 SYNCHROTRON DIAMOND BEAMLINE I03 1.73937 Diamond I03 3 SYNCHROTRON DIAMOND BEAMLINE I03 1.74380 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 64.99 100 0.107 0.111 0.024 0.999 15.4 21.3 35601 2 20.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 99.9 0.839 0.876 0.188 0.904 3.7 21.4
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 1R03 1.6 64.99 33807 1772 99.9 0.1565 0.1553 0.1791 0.1765 RANDOM 22.355
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.803 r_dihedral_angle_4_deg 12.942 r_dihedral_angle_3_deg 12.211 r_dihedral_angle_1_deg 5.351 r_angle_refined_deg 1.548 r_chiral_restr 0.091 r_gen_planes_refined 0.01 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1407 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling MOLREP phasing