8OEI
SFX structure of FutA after an accumulated dose of 350 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 |
2.08 | 40.98 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 39.366 | α = 90 |
b = 78.22 | β = 97.903 |
c = 48.025 | 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 | 298 | CCD | MPCCD | 2022-05-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | FREE ELECTRON LASER | SACLA BEAMLINE BL2 | 1.126 | SACLA | BL2 |
Serial Crystallography
Sample delivery method | ||
---|---|---|
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 |
Measurement | |||||
---|---|---|---|---|---|
Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
1 | 10 | 30 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.65 | 32.441 | 100 | 0.97 | 0.134 | 3.7 | 165.2 | 34653 | 20.98 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.65 | 1.679 | 100 | 0.691 | 0.4 | 0.43 | 82.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.65 | 32.441 | 34653 | 1786 | 99.957 | 0.161 | 0.1599 | 0.1885 | 27.641 |
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] | |
0.295 | -0.303 | 0.161 | -0.358 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_6_deg | 15.86 |
r_dihedral_angle_3_deg | 12.708 |
r_lrange_it | 7.073 |
r_lrange_other | 7.071 |
r_dihedral_angle_1_deg | 6.182 |
r_scangle_it | 6.13 |
r_scangle_other | 6.129 |
r_dihedral_angle_2_deg | 5.619 |
r_scbond_it | 3.834 |
r_scbond_other | 3.831 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2460 |
Nucleic Acid Atoms | |
Solvent Atoms | 107 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DIALS | data reduction |
cctbx.xfel.merge | data scaling |
MOLREP | phasing |