9BN8
Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli in complex with UMA and inhibitor A19
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 | 65.488, 65.488, 134.764 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 58.900 - 1.350 |
| R-factor | 0.1339 |
| Rwork | 0.133 |
| R-free | 0.15750 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.007 |
| RMSD bond angle | 0.919 |
| 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] | 67.380 | 1.390 |
| High resolution limit [Å] | 1.350 | 1.350 |
| Rmerge | 0.069 | 1.317 |
| Rmeas | 0.072 | 1.388 |
| Rpim | 0.019 | 0.435 |
| Total number of observations | 1676743 | 91897 |
| Number of reflections | 124023 | 9171 |
| <I/σ(I)> | 17.7 | 1.8 |
| Completeness [%] | 100.0 | |
| Redundancy | 13.5 | 10 |
| CC(1/2) | 1.000 | 0.682 |
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-0401, Cryo: 2.5M Lithium Sulfate + 2mM inhibitor A19 |
