7MYC
Structure of proline utilization A with the FAD covalently modified by tetrahydrothiophene
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ALS BEAMLINE 4.2.2 |
Synchrotron site | ALS |
Beamline | 4.2.2 |
Temperature [K] | 100 |
Detector technology | CMOS |
Collection date | 2019-10-22 |
Detector | RDI CMOS_8M |
Wavelength(s) | 1.00003 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 100.932, 101.496, 125.741 |
Unit cell angles | 90.00, 106.54, 90.00 |
Refinement procedure
Resolution | 45.650 - 1.900 |
R-factor | 0.1781 |
Rwork | 0.176 |
R-free | 0.21890 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 5kf6 |
Data reduction software | XDS |
Data scaling software | Aimless (0.7.4) |
Phasing software | PHENIX |
Refinement software | PHENIX (1.19.2) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 48.380 | 48.380 | 1.930 |
High resolution limit [Å] | 1.900 | 10.410 | 1.900 |
Rmerge | 0.099 | 0.026 | 1.159 |
Rmeas | 0.117 | 0.031 | 1.378 |
Rpim | 0.061 | 0.016 | 0.737 |
Total number of observations | 677886 | 4262 | 32523 |
Number of reflections | 189522 | 1194 | 9411 |
<I/σ(I)> | 8.7 | 28.7 | 1 |
Completeness [%] | 99.1 | 96.5 | 99.9 |
Redundancy | 3.6 | 3.6 | 3.5 |
CC(1/2) | 0.996 | 0.999 | 0.453 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 286 | Protein stock solution: 6 mg/mL PutA with 50 mM tetrahydrothiophene-2-carboxylate in a buffer containing 50 mM Tris (pH 8.0), 50 mM NaCl, 5% (w/v) glycerol, and 0.5 mM Tris(2-caboxyethyl)phosphine. Reservoir solution: 19 % PEG-3350, 0.2 M ammonium sulfate, 0.1 M magnesium chloride, 0.1 M HEPES (pH 8.0), and 0.1 M sodium formate. Cryo-buffer: reservoir supplemented with 15 % PEG-200. Crystals were grown in low-light conditions and then exposed to bright light before flash-cooling to induce the decarboxylation of tetrahydrothiophene-2-carboxylate and covalent modification of the FAD |