7O6D
Crystal structure of human mitochondrial ferritin (hMTF) Fe(II)-loaded for 3 minutes under anaerobic environment
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 | 61.06 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 184.09 | α = 90 |
b = 184.09 | β = 90 |
c = 184.09 | 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 PILATUS 6M-F | 2019-05-17 | M | MAD | ||||||
2 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M-F | 2019-05-17 | M | MAD | ||||||
3 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M-F | 2019-05-17 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.90001 | Diamond | I04 |
2 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 1.73892 | Diamond | I04 |
3 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 1.75120 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.47 | 29.11 | 100 | 0.108 | 0.113 | 0.024 | 0.999 | 14.6 | 21.9 | 45819 | 2 | 15.7 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.47 | 1.55 | 100 | 0.671 | 0.702 | 0.151 | 0.932 | 4.2 | 21.4 |
Refinement
Statistics | |||||||||||||||||||
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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 | 1.47 | 28.09 | 43580 | 2229 | 99.94 | 0.1466 | 0.146 | 0.1571 | RANDOM | 19.047 |
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 | 38.5 |
r_dihedral_angle_4_deg | 12.924 |
r_dihedral_angle_3_deg | 12.384 |
r_dihedral_angle_1_deg | 5.058 |
r_angle_refined_deg | 1.367 |
r_chiral_restr | 0.093 |
r_gen_planes_refined | 0.008 |
r_bond_refined_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1406 |
Nucleic Acid Atoms | |
Solvent Atoms | 398 |
Heterogen Atoms | 19 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
SCALA | data scaling |
MOLREP | phasing |