7TOT
Crystal Structure of pantothenate synthetase from Bartonella henselae
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | Protein at 21 mg/mL was mixed 1:1 (0.4 uL protein and 0.4 uL precipitant) with 12.5% w/v PEG 1000, 12.5% w/v PEG3350, 12.5% v/v MPD, 0.03 M each sodium nitrate, disodium hydrogen phosphate, and ammonium sulfate, and 0.1 M MES/imidazole pH 7.5 (Morpheus C8). Cryo: Direct. Tray: 320104c8: pin: ifl7-5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.58 | 52.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 45.82 | α = 108.9 |
b = 51.26 | β = 99.37 |
c = 78.65 | γ = 90.6 |
Symmetry | |
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Space Group | P 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 | 100 | CCD | RAYONIX MX-300 | Beryllium Lenses | 2021-04-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 1.8 | 35.35 | 94.9 | 0.023 | 0.031 | 0.999 | 19.95 | 2.193 | 58720 | 29 |
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) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.8 | 1.85 | 94.7 | 0.349 | 0.47 | 0.895 | 2.7 | 2.214 |
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 | THROUGHOUT | 2ejc | 1.8 | 35.35 | 1.98 | 58669 | 2089 | 94.92 | 0.1798 | 0.1786 | 0.216 | 45.4034 |
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 | 4316 |
Nucleic Acid Atoms | |
Solvent Atoms | 373 |
Heterogen Atoms | 70 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
MoRDa | phasing |