6TR9
Crystal structure of human L ferritin (HuLf) triple variant E60A-E61A-E64A
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5LG8 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 293 | 80 mM cadmium nitrate, 80 mM ammonium sulfate, 200 mM sodium acetate, pH 4.6 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.69 | 66.63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 151.215 | α = 90 |
b = 151.215 | β = 90 |
c = 151.215 | γ = 90 |
Symmetry | |
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Space Group | I 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 | 2018-04-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.91587 | Diamond | I04-1 |
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 | 2.46 | 75.61 | 100 | 0.106 | 0.112 | 0.024 | 1 | 21.2 | 21.2 | 11055 | 2 | 50.2 |
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 | 2.46 | 2.59 | 100 | 1.044 | 1.09 | 0.233 | 0.929 | 3.1 | 21.6 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 5LG8 | 2.46 | 61.81 | 10926 | 581 | 98.869 | 0.204 | 0.2005 | 0.2579 | 47.624 |
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 | 35.271 |
r_dihedral_angle_4_deg | 23.051 |
r_dihedral_angle_3_deg | 16.807 |
r_lrange_it | 9.876 |
r_lrange_other | 9.819 |
r_scangle_it | 8.237 |
r_scangle_other | 8.234 |
r_mcangle_other | 6.152 |
r_mcangle_it | 6.148 |
r_scbond_it | 5.834 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1364 |
Nucleic Acid Atoms | |
Solvent Atoms | 109 |
Heterogen Atoms | 7 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
MOLREP | phasing |