7O67
Crystal structure of human mitochondrial ferritin (hMTF) Fe(II)-loaded for 15 minutes showing either a dioxygen or a superoxide anion coordinated to iron ions in the ferroxidase site
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1R03 |
Crystallization
Crystalization Experiments | ||||
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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 | |
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Matthews coefficient | Solvent content |
3.16 | 61.12 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 184.184 | α = 90 |
b = 184.184 | β = 90 |
c = 184.184 | γ = 90 |
Symmetry | |
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Space Group | F 4 3 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | 0.97625 | 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 | 1.86 | 106.34 | 99.8 | 0.099 | 0.108 | 0.033 | 0.998 | 12.4 | 10.4 | 22955 | 2 | 24.4 |
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 | 1.86 | 1.96 | 100 | 0.601 | 0.651 | 0.196 | 0.906 | 3.4 | 10.8 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1R03 | 1.86 | 46.09 | 21613 | 1164 | 98.72 | 0.1733 | 0.1706 | 0.2237 | RANDOM | 27.859 |
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 | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.823 |
r_dihedral_angle_3_deg | 13.26 |
r_dihedral_angle_4_deg | 12.589 |
r_dihedral_angle_1_deg | 5.536 |
r_angle_refined_deg | 1.59 |
r_chiral_restr | 0.102 |
r_bond_refined_d | 0.009 |
r_gen_planes_refined | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1399 |
Nucleic Acid Atoms | |
Solvent Atoms | 240 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
SCALA | data scaling |
MOLREP | phasing |