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Crystal structure of human mitochondrial ferritin (hMTF) Fe(II)-loaded for 90 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 3.2 61.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.271 α = 90 b = 184.271 β = 90 c = 184.271 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 PILATUS 6M-F 2018-09-07 M MAD 2 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2018-09-07 M MAD 3 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2018-09-07 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04 2 SYNCHROTRON DIAMOND BEAMLINE I04 1.73840 Diamond I04 3 SYNCHROTRON DIAMOND BEAMLINE I04 1.75120 Diamond I04
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 1.7 92.13 100 0.143 0.149 0.034 0.998 12.3 18.6 30053 2 14.4
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 1.7 1.79 100 0.717 0.751 0.173 0.925 3.6 18.6
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 1R03 1.7 65.23 28500 1513 99.86 0.1565 0.1552 0.1553 0.181 0.1814 RANDOM 19.651
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 35.197 r_dihedral_angle_4_deg 13.993 r_dihedral_angle_3_deg 12.469 r_dihedral_angle_1_deg 5.245 r_angle_refined_deg 1.621 r_chiral_restr 0.105 r_bond_refined_d 0.01 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1407 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling MOLREP phasing