7RAG
Structure of the CwlD amidase from Clostridioides difficile in complex with the GerS lipoprotein
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 291 | 12-18 % PEG 3350, 5 % glycerol, 0.25 M ammonium nitrate, 50 mM BisTris pH 7.5. 1:1 ratio of reservoir to 30 mg/ml complex |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.72 | 54.77 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 105.185 | α = 90 |
b = 105.185 | β = 90 |
c = 154.771 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 2 |
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 PILATUS3 6M | mirrors | 2020-03-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 0.9794 | APS | 23-ID-D |
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 | 2.4 | 46 | 99.9 | 0.109 | 0.115 | 0.036 | 0.999 | 10.7 | 10.2 | 37392 |
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 | 2.4 | 2.49 | 98.9 | 2.205 | 2.329 | 0.745 | 0.406 | 1.1 | 9.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MIR | THROUGHOUT | 2.4 | 45.55 | 1.33 | 37340 | 3742 | 99.72 | 0.2076 | 0.203 | 0.249 | 69.1844 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2890 |
Nucleic Acid Atoms | |
Solvent Atoms | 14 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
PROTEUM PLUS | data reduction |
PROTEUM PLUS | data scaling |
SHARP | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |