8DCN
Crystal structure of Clostridioides difficile binary toxin CDTb D4 fragment in complex with BINTOXB/9 Fab
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 295 | 10.1% PEG3350, 13.4% 2-propanol, 0.2 M ammonium citrate pH 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.15 | 60.99 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 98.209 | α = 90 |
b = 111.76 | β = 90 |
c = 148.349 | γ = 90 |
Symmetry | |
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Space Group | P 21 2 21 |
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 | 80 | CCD | ADSC QUANTUM 315r | 2020-11-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.979 | APS | 19-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.6 | 55.88 | 99.2 | 0.99 | 8.2 | 5.7 | 50515 | 58.05 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.6 | 2.69 | 0.61 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6UWT | 2.6 | 55.88 | 1.34 | 50515 | 2482 | 99.21 | 0.2281 | 0.2265 | 0.2603 | 64.54 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.6159 |
f_angle_d | 0.5812 |
f_chiral_restr | 0.0425 |
f_plane_restr | 0.005 |
f_bond_d | 0.0026 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8644 |
Nucleic Acid Atoms | |
Solvent Atoms | 79 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
Coot | model building |
PHENIX | refinement |
iMOSFLM | data reduction |
Aimless | data scaling |
PHASER | phasing |