8PP5
Unitary crystal structure of positively supercharged ferritin variant Ftn(pos)-m1 (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 | 6H6U |
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 Formate Ftn(pos)-m1: 4 mg/mL in 50mM Tris pH 7.5 0.9 M NaCl 2microliter reservoir + 1microliter Ftn(pos)-m1 +1 microliterL 50mM Tris pH 7.5 0.3 M NaCl |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.1 | 60.29 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 126.898 | α = 90 |
b = 126.898 | β = 90 |
c = 187.468 | γ = 90 |
Symmetry | |
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Space Group | I 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 EIGER X 16M | 2021-09-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 0.97625 | PETRA III, EMBL c/o DESY | P13 (MX1) |
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 | 1.75 | 105.09 | 98.9 | 0.174 | 0.193 | 0.082 | 0.997 | 8.3 | 10.5 | 145913 |
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 | 1.75 | 1.78 | 3.671 | 4.335 | 2.24 | 0.184 | 6.4 |
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 | 2 | 105.086 | 99602 | 4906 | 99.991 | 0.162 | 0.1603 | 0.1925 | 26.449 |
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] | |
0.545 | 0.545 | -1.09 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_6_deg | 17.117 |
r_dihedral_angle_3_deg | 14.558 |
r_dihedral_angle_2_deg | 9.773 |
r_lrange_it | 7.412 |
r_lrange_other | 7.371 |
r_scangle_it | 6.464 |
r_scangle_other | 6.463 |
r_dihedral_angle_1_deg | 5.605 |
r_scbond_it | 4.165 |
r_scbond_other | 4.165 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8568 |
Nucleic Acid Atoms | |
Solvent Atoms | 916 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
XDS | data scaling |
xia2 | data scaling |
MOLREP | phasing |