8OGG
Crystal structure of FutA after an accumulated dose of 5 kGy
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2VP1 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 294 | Purified protein, diluted crystal seeds, and crystallisation buffer were mixed at a 1:1.5:1.5 ratio. Crystallisation buffer was 25% PEG 3350, 200 mM sodium thiocyanate. Crystal seed stock was diluted 1:20 in 25% PEG 3350. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.13 | 42.27 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 39.718 | α = 90 |
b = 78.66 | β = 97.788 |
c = 48.382 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | 294 | PIXEL | DECTRIS PILATUS3 6M | 2018-01-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.968 | Diamond | I24 |
Serial Crystallography
Sample delivery method | ||
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Diffraction ID | Description | Sample Delivery Method |
1 | fixed target |
Fixed Target | ||||||
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Diffraction ID | Description | Sample Holding | Support Base | Motion control | Sample Solvent | |
1 | Silicon nitride chip | 25600 apertures |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | R Split (All) | 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 | 1.76 | 40.97 | 100 | 0.931 | 0.923 | 0.235 | 3.1 | 26.23 | 29256 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.76 | 1.79 | 0.93 | 0.431 | 0.684 | 0.41 | 19.1 |
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 | 1.76 | 40.97 | 29256 | 1503 | 99.956 | 0.204 | 0.2017 | 0.2413 | 31.339 |
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] | |
0.187 | -0.219 | -0.089 | -0.037 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.678 |
r_dihedral_angle_4_deg | 14.817 |
r_dihedral_angle_3_deg | 14.53 |
r_dihedral_angle_1_deg | 6.515 |
r_lrange_other | 5.95 |
r_lrange_it | 5.948 |
r_scangle_it | 4.547 |
r_scangle_other | 4.546 |
r_mcangle_it | 2.889 |
r_mcangle_other | 2.889 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2462 |
Nucleic Acid Atoms | |
Solvent Atoms | 81 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
REFMAC | refinement |
DIALS | data reduction |
cctbx.prime | data scaling |
MOLREP | phasing |