7KDN
Crystal structure of Acetyl-CoA Synthetase in Complex with Adenosine-5'-propylphosphate from Aspergillus fumigatus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 287 | RigakuReagents Morpheus screen, g9:10% w/v PEG 20000, 20% v/v PEG MME 550, 0.02M carboxylic acids (sodium formate, ammonium acetate, trisodium citrate,sodium potassium L-tartrate, sodium oxamate, 0.1M bicine/Trizma base pH8.5; AsfuA.00629.a.FS11.PD00486 at 10 mg/ml, 1mM TCEP, 1mM BSI5663/Propyl-AMP; cryo: direct; tray 313288g9, puck ejj3-5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.34 | 47.58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 103.79 | α = 68.15 |
b = 104.21 | β = 66.55 |
c = 125.65 | γ = 62.22 |
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 | 2019-11-14 | 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 | 2.8 | 50 | 97.9 | 0.12 | 0.139 | 0.996 | 10.14 | 3.9 | 100485 | -3 | 57.775 |
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 | 2.8 | 2.87 | 97.5 | 0.937 | 1.083 | 0.703 | 1.57 | 4 |
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 | 5IFI | 2.8 | 47.92 | 1.97 | 100431 | 1999 | 98.06 | 0.2161 | 0.2155 | 0.2462 | 65.7636 |
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 | 26431 |
Nucleic Acid Atoms | |
Solvent Atoms | 43 |
Heterogen Atoms | 156 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHASER | phasing |
Coot | model building |