7UXG
Crystal structure of putative serine protease YdgD from Escherichia coli
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | APS BEAMLINE 19-ID |
| Synchrotron site | APS |
| Beamline | 19-ID |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2021-08-10 |
| Detector | DECTRIS PILATUS 6M |
| Wavelength(s) | 0.978 |
| Spacegroup name | P 65 |
| Unit cell lengths | 98.145, 98.145, 43.441 |
| Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
| Resolution | 42.500 - 2.240 |
| R-factor | 0.2608 |
| Rwork | 0.258 |
| R-free | 0.30980 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | Alphafold2 |
| RMSD bond length | 0.004 |
| RMSD bond angle | 0.755 |
| Data reduction software | HKL-3000 |
| Data scaling software | HKL-3000 |
| Phasing software | PHENIX |
| Refinement software | PHENIX (1.20_4459) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 50.000 | 2.290 |
| High resolution limit [Å] | 2.240 | 2.250 |
| Rmerge | 0.048 | 1.585 |
| Rpim | 0.011 | 0.392 |
| Number of reflections | 11646 | 584 |
| <I/σ(I)> | 1.78 | 1.52 |
| Completeness [%] | 100.0 | 99.8 |
| Redundancy | 19.7 | 16.8 |
| CC(1/2) | 0.755 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 298 | 25% PEG 3350, 0.2 M NaCl, 0.1 M Hepes pH 7.5 |
