8BIQ
Crystal structure of acyl-COA synthetase from Metallosphaera sedula in complex with acetyl-AMP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.2 | 293 | Drops of 3 mg/ml protein solution dispensed with a Mosquito robot into MRC-SD2 plates containing commercial screens with different ratios (1.25:0.75, 0.75:1.25). Best crystals grown in 0.1M acetic acid pH 5.2, 200mM NaCl, 7-10% PEG3350. Crystals appeared after 24h. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.24 | 45.01 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 100.864 | α = 90 |
b = 88.289 | β = 92.97 |
c = 131.207 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | PIXEL | DECTRIS EIGER2 X 16M | 2019-04-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9795 | Diamond | I04 |
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 | 2.8 | 66.48 | 99.7 | 0.165 | 0.234 | 0.165 | 0.962 | 3.2 | 1.9 | 56843 |
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 | 2.8 | 2.88 | 99.9 | 0.817 | 1.156 | 0.817 | 0.527 | 1.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3B7W | 2.8 | 66.48 | 54003 | 2810 | 99.68 | 0.23648 | 0.23456 | 0.27325 | RANDOM | 60.627 |
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] | |
1.37 | -0.47 | -1.28 | -0.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 17.468 |
r_dihedral_angle_2_deg | 14.22 |
r_dihedral_angle_1_deg | 7.708 |
r_long_range_B_refined | 5.865 |
r_long_range_B_other | 5.865 |
r_scangle_other | 2.919 |
r_mcangle_it | 2.457 |
r_mcangle_other | 2.456 |
r_angle_refined_deg | 2.048 |
r_scbond_it | 1.733 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 18032 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 95 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
DIALS | data reduction |
PHASER | phasing |