8PU5
Crystal structure of the Acyl-CoA dehydrogenase FadE1(PA0506) E441A from Pseudomonas aeruginosa complexed with C16CoA
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 298 | 0.1M Bis Tris Propane pH 6.5, 0.2M sodium nitrate, 20% w/v PEG 3350, 10% v/v ethylene glycol, 5mM C16CoA |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.45 | 49.74 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 92.955 | ¦Á = 90 |
b = 92.955 | ¦Â = 90 |
c = 128.782 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 31 1 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 EIGER2 XE 9M | 2021-11-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.92 | Diamond | I04-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.44 | 128.78 | 100 | 0.194 | 0.197 | 0.031 | 0.999 | 11.5 | 38.5 | 114956 | 15.1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.44 | 1.46 | 100 | 4.451 | 4.529 | 0.834 | 0.3 | 0.4 | 29.3 |
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 (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.44 | 80.63 | 109044 | 5767 | 99.92 | 0.1861 | 0.18462 | 0.1943 | 0.21378 | 0.2176 | RANDOM | 22.81 |
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] | |
-0.32 | -0.16 | -0.32 | 1.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.731 |
r_dihedral_angle_4_deg | 18.008 |
r_dihedral_angle_3_deg | 13.711 |
r_dihedral_angle_1_deg | 5.931 |
r_long_range_B_refined | 5.706 |
r_long_range_B_other | 5.596 |
r_scangle_other | 4.449 |
r_scbond_it | 3.004 |
r_scbond_other | 3.003 |
r_mcangle_it | 2.289 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4563 |
Nucleic Acid Atoms | |
Solvent Atoms | 421 |
Heterogen Atoms | 107 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHASER | phasing |
xia2 | data scaling |
xia2 | data reduction |