8RPL
AMP-forming acetyl-CoA synthetase from Chloroflexota bacterium with bound acetyl AMP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 2 uL (protein in 50 mM HEPES pH 7.5, 100 mM KCl) + 2 uL (25% PEG 400, 0.1 M Na-MES, pH 6.5, 0.05 M MnCl2 or MgCl2) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4 | 64.62 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 161.909 | α = 90 |
b = 161.909 | β = 90 |
c = 817.234 | γ = 120 |
Symmetry | |
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Space Group | H 3 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 EIGER X 16M | Si111 | 2023-09-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 0.97630 | PETRA III, EMBL c/o DESY | P13 (MX1) |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.37 | 50 | 99.9 | 0.142 | 0.146 | 0.999 | 16 | 20.4 | 167479 | -3 | 70 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.37 | 2.56 | 100 | 2.9 | 2.97 | 0.502 | 1.13 | 21.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.37 | 48.304 | 167354 | 8378 | 99.868 | 0.163 | 0.1613 | 0.2007 | 76.265 |
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] | |
0.658 | 0.329 | 0.658 | -2.134 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 14.905 |
r_dihedral_angle_6_deg | 14.338 |
r_dihedral_angle_2_deg | 9.946 |
r_dihedral_angle_other_2_deg | 9.47 |
r_lrange_it | 9.01 |
r_lrange_other | 9.01 |
r_scangle_it | 7.511 |
r_scangle_other | 7.511 |
r_dihedral_angle_1_deg | 7.046 |
r_mcangle_it | 5.312 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 19931 |
Nucleic Acid Atoms | |
Solvent Atoms | 181 |
Heterogen Atoms | 168 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |