7O68
Crystal structure of human mitochondrial ferritin (hMTF) Fe(II)-loaded for 120 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 | ||||
---|---|---|---|---|
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 |
3.18 | 61.29 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 183.787 | α = 90 |
b = 183.787 | β = 90 |
c = 183.787 | γ = 90 |
Symmetry | |
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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 | 1.68 | 64.98 | 100 | 0.114 | 0.119 | 0.026 | 0.998 | 17.9 | 21.3 | 30852 | 2 | 12.3 |
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 | 1.68 | 1.77 | 100 | 0.711 | 0.741 | 0.159 | 0.934 | 4.5 | 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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1R03 | 1.68 | 64.98 | 29280 | 1558 | 99.98 | 0.1587 | 0.1575 | 0.1831 | RANDOM | 18.016 |
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 | 34.547 |
r_dihedral_angle_3_deg | 12.812 |
r_dihedral_angle_4_deg | 11.676 |
r_dihedral_angle_1_deg | 5.519 |
r_angle_refined_deg | 1.589 |
r_chiral_restr | 0.096 |
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 | 324 |
Heterogen Atoms | 18 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
SCALA | data scaling |
MOLREP | phasing |