8VJ3
Crystal Structure of Betaine aldehyde dehydrogenase (BetB) from Klebsiella aerogenes (FAD bound)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 291 | Berkeley C10: 100 mM Sodium acetate / Hydrochloric acid pH 4.5, 100 mM Ammonium phosphate dibasic, 20% (w/v) PEG 3350, 5% (v/v) 2-Propanol, KlaeA.00020.b.B1.PW39167 at 17 mg/mL. 5mM FAD soak for 4 hours. 3 of the 4 subunits have disordered FAD in the nicotinamide ring so they appear as ADP. Plate 13676 well C10 drop 1. Puck: PSL-0803, Cryo: 30% PEG3350 + 70% crystallant. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.41 | 49.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 84.007 | α = 90 |
b = 100.789 | β = 96.09 |
c = 123.938 | 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 XE 9M | 2023-12-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 19-ID | 0.9785 | NSLS-II | 19-ID |
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 | 1.9 | 47.25 | 99.9 | 0.112 | 0.121 | 0.046 | 0.998 | 11.5 | 6.9 | 161437 |
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 | 1.9 | 1.95 | 100 | 1.145 | 1.241 | 0.473 | 0.717 | 6.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.9 | 47.25 | 1.33 | 161373 | 8140 | 99.91 | 0.1583 | 0.157 | 0.1828 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.15 |
f_angle_d | 0.861 |
f_chiral_restr | 0.053 |
f_plane_restr | 0.011 |
f_bond_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14767 |
Nucleic Acid Atoms | |
Solvent Atoms | 1138 |
Heterogen Atoms | 186 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
Aimless | data scaling |
XDS | data reduction |
PHASER | phasing |