8AAV
Human heavy chain ferritin with introduced Cys residues modified with C10 ligand
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 298 | Crystallization of little amounts of protein or functionalized protein variants were performed via hanging drop vapor diffusion techniques. Reservoir solution (100 mM Tris, 500 mM MgOAc, pH 8.5) was prepared in a 24- well manual plate set. Drops were prepared on siliconized glass cover slides (Jena Bioscience) by mixing 2 microL reservoir solutions with 1 microL 50 mM Tris, 1 M NaCl, pH 7.5 buffer and 1 microL of respective ferritin variant. Plates were incubated at 298K. After one day first crystals were visible. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.95 | 58.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 181.44 | α = 90 |
b = 181.44 | β = 90 |
c = 181.44 | γ = 90 |
Symmetry | |
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Space Group | P 2 3 |
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 EIGER R 4M | 2021-08-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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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 | 2 | 48.54 | 99.9 | 0.052 | 0.054 | 0.012 | 1 | 43.2 | 20.9 | 132696 |
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 | 2.03 | 98.5 | 0.181 | 0.186 | 0.041 | 0.995 | 20.2 |
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 | 5JKK | 2 | 48.54 | 131264 | 2101 | 99.86 | 0.1449 | 0.1444 | 0.177 | RANDOM | 16.458 |
Temperature Factor Modeling | ||||||
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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 | 38.293 |
r_dihedral_angle_4_deg | 20.865 |
r_dihedral_angle_3_deg | 11.787 |
r_dihedral_angle_1_deg | 5.311 |
r_angle_refined_deg | 1.675 |
r_angle_other_deg | 1.508 |
r_chiral_restr | 0.092 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.01 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11301 |
Nucleic Acid Atoms | |
Solvent Atoms | 1076 |
Heterogen Atoms | 135 |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHASER | phasing |