6X99
Structure of proline utilization A with D-proline bound in the L-glutamate-gamma-semialdehyde dehydrogenase active site
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 | 2020-02-11 |
Detector | RDI CMOS_8M |
Wavelength(s) | 0.9762 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 101.208, 102.316, 127.032 |
Unit cell angles | 90.00, 106.42, 90.00 |
Refinement procedure
Resolution | 46.075 - 1.560 |
R-factor | 0.1757 |
Rwork | 0.174 |
R-free | 0.20370 |
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 (1.14) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 46.080 | 46.080 | 1.590 |
High resolution limit [Å] | 1.560 | 8.540 | 1.560 |
Rmerge | 0.082 | 0.021 | 1.272 |
Rmeas | 0.097 | 0.025 | 1.504 |
Rpim | 0.050 | 0.013 | 0.795 |
Total number of observations | 1255558 | 7850 | 60757 |
Number of reflections | 350164 | 2200 | 17275 |
<I/σ(I)> | 8.1 | 29.8 | 0.6 |
Completeness [%] | 99.5 | 98.3 | 99 |
Redundancy | 3.6 | 3.6 | 3.5 |
CC(1/2) | 0.998 | 0.999 | 0.374 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 286 | Crystallization experiments were set up with SmPutA (6 mg/mL) and D-proline (50 mM) 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. Crystals were grown using a reservoir solution containing 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. Cryobuffer: reservoir supplemented with 15 % PEG-200 |