Crystal structure of Horse spleen L-ferritin mutant (E53F/E56F/E57F/R59F/E60F/E63F)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1DAT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 293 | Ammonium sulfate, Cadmium sulfate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.12 | 60.55 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 181.43 | α = 90 |
b = 181.43 | β = 90 |
c = 181.43 | 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 | 93 | PIXEL | RIGAKU HyPix-6000HE | 2022-02-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E DW | 1.54184 |
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 | 1.5 | 19.91 | 99.9 | 0.07 | 0.073 | 0.019 | 0.999 | 24.5 | 12.4 | 41371 |
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 | 1.5 | 1.53 | 99.2 | 0.771 | 0.824 | 0.284 | 0.867 | 2.3 | 8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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) | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1DAT | 1.5 | 19.91 | 1.33 | 40919 | 2073 | 98.87 | 0.1861 | 0.1852 | 0.1877 | 0.2026 | 0.206 |
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 |
f_dihedral_angle_d | 13.483 |
f_angle_d | 1.649 |
f_chiral_restr | 0.086 |
f_plane_restr | 0.018 |
f_bond_d | 0.013 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1388 |
Nucleic Acid Atoms | |
Solvent Atoms | 212 |
Heterogen Atoms | 21 |
Software
Software | |
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Software Name | Purpose |
CrysalisPro | data collection |
CrysalisPro | data reduction |
Aimless | data scaling |
MOLREP | phasing |
REFMAC | refinement |
Coot | model building |