7MY9
Structure of proline utilization A with 1,3-dithiolane-2-carboxylate bound in the proline dehydrogenase active site
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 24-ID-C |
Synchrotron site | APS |
Beamline | 24-ID-C |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2019-11-02 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.979100 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 101.932, 103.094, 126.906 |
Unit cell angles | 90.00, 106.50, 90.00 |
Refinement procedure
Resolution | 121.682 - 1.628 |
R-factor | 0.1637 |
Rwork | 0.162 |
R-free | 0.19210 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 5kf6 |
Data reduction software | XDS |
Data scaling software | Aimless (0.5.32) |
Phasing software | PHENIX |
Refinement software | PHENIX (1.14) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 121.682 | 121.680 | 1.660 |
High resolution limit [Å] | 1.628 | 8.920 | 1.630 |
Rmerge | 0.053 | 0.020 | 0.723 |
Rmeas | 0.061 | 0.023 | 0.851 |
Rpim | 0.031 | 0.011 | 0.441 |
Total number of observations | 7889 | 50183 | |
Number of reflections | 309107 | 1984 | 14533 |
<I/σ(I)> | 14.5 | 50.4 | 1.5 |
Completeness [%] | 98.5 | 97.9 | 93.7 |
Redundancy | 3.8 | 4 | 3.5 |
CC(1/2) | 0.999 | 0.999 | 0.628 |
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 1,3-dithiolane-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 and harvested in low-light conditions |