8PP4
Binary crystal structure of positively supercharged ferritin variant Ftn(pos) and reduced charge negatively supercharged ferritin variant Ftn(neg)-m3 (Mg formate condition)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2CEI | Human Heavy Chain Ferritin |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293.15 | reservoir: 0.19M Magnesium FormateFtn(pos): 4 mg/mL in 50mM Tris pH 7.5 1 M NaClFtn(Wildtype): 4mg/mL in 50mM Tris pH 7.5 0.3 M NaCl2 uL reservoir + 1uL Ftn(pos) + 1uL Ftn(neg)-m3 added to coverslide in this order. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.79 | 55.88 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 127.039 | α = 90 |
b = 127.039 | β = 90 |
c = 176.961 | γ = 90 |
Symmetry | |
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Space Group | P 4 |
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 EIGER2 X 16M | 2021-06-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, DESY BEAMLINE P11 | 1.0332 | PETRA III, DESY | P11 |
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 | 1.99 | 49.356 | 99.9 | 0.037 | 0.052 | 0.037 | 0.999 | 12.1 | 2 | 188549 |
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 | 2 | 2.03 | 0.392 | 0.555 | 0.392 | 0.749 | 2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | FREE R-VALUE | 1.999 | 49.356 | 188548 | 9438 | 99.872 | 0.183 | 0.1814 | 0.2207 | 34.171 |
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] | |
-0.898 | -0.898 | 1.796 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.968 |
r_dihedral_angle_4_deg | 19.79 |
r_dihedral_angle_3_deg | 13.932 |
r_lrange_other | 8.812 |
r_lrange_it | 8.802 |
r_dihedral_angle_1_deg | 5.881 |
r_scangle_it | 5.614 |
r_scangle_other | 5.614 |
r_scbond_it | 3.732 |
r_scbond_other | 3.732 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 17107 |
Nucleic Acid Atoms | |
Solvent Atoms | 896 |
Heterogen Atoms | 24 |
Software
Software | |
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Software Name | Purpose |
xia2 | data scaling |
XDS | data scaling |
Aimless | data scaling |
PHASER | phasing |
Coot | model building |
REFMAC | refinement |