9BN9
Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli in complex with UMA and two inhibitor A19 molecules
This is a non-PDB format compatible entry.
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | NSLS-II BEAMLINE 19-ID |
| Synchrotron site | NSLS-II |
| Beamline | 19-ID |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2024-04-13 |
| Detector | DECTRIS EIGER2 XE 9M |
| Wavelength(s) | 0.9786 |
| Spacegroup name | P 41 |
| Unit cell lengths | 65.381, 65.381, 134.681 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 58.820 - 1.230 |
| R-factor | 0.1242 |
| Rwork | 0.123 |
| R-free | 0.14240 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.006 |
| RMSD bond angle | 0.926 |
| Data reduction software | XDS |
| Data scaling software | Aimless |
| Phasing software | PHASER |
| Refinement software | PHENIX ((dev_5318: ???)) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 67.340 | 1.260 |
| High resolution limit [Å] | 1.230 | 1.230 |
| Rmerge | 0.048 | 0.756 |
| Rmeas | 0.050 | 0.854 |
| Rpim | 0.014 | 0.387 |
| Total number of observations | 1877914 | 42363 |
| Number of reflections | 159202 | 9248 |
| <I/σ(I)> | 22.8 | 1.7 |
| Completeness [%] | 97.6 | |
| Redundancy | 11.8 | 4.6 |
| CC(1/2) | 1.000 | 0.646 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 291 | 1.9M ammonium sulfate, 7% (v/v) PEG 400, 0.1M Hepes 7.5. EscoA.17938.a.AE1.PW39153 at 17.4 mg/mL. Soaked with 2mM A19 in crystallant (10 ul) for 2h, and transferred to another 10 ul of the same solution for another 2h. plate Liu-Lim-116 A2. Puck: PSL-0407, Cryo: 2.5M Lithium Sulfate + 2mM inhibitor A19 |
