9DQW
Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli in complex with UMA and AMP-PNP
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 | 2024-03-24 |
| Detector | DECTRIS EIGER2 XE 9M |
| Wavelength(s) | 0.9786 |
| Spacegroup name | P 41 |
| Unit cell lengths | 65.441, 65.441, 135.609 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 47.090 - 1.450 |
| R-factor | 0.1505 |
| Rwork | 0.150 |
| R-free | 0.16470 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.008 |
| RMSD bond angle | 1.004 |
| Data reduction software | XDS |
| Data scaling software | Aimless |
| Phasing software | PHASER |
| Refinement software | PHENIX ((dev_5462: ???)) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 47.090 | 1.470 |
| High resolution limit [Å] | 1.450 | 1.450 |
| Rmerge | 0.087 | 1.686 |
| Rmeas | 0.090 | 1.753 |
| Rpim | 0.025 | 0.478 |
| Total number of observations | 1297494 | 65654 |
| Number of reflections | 100616 | 4968 |
| <I/σ(I)> | 15.6 | 1.7 |
| Completeness [%] | 100.0 | |
| Redundancy | 12.9 | 13.2 |
| CC(1/2) | 0.999 | 0.640 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 291 | 2.0 M ammonium sulfate, 0.1 Hepes pH 7.5, 7% (v/v) PEG 400. EscoA.17938.a.AE1.PW39153 at 17.4 mg/mL. Soaked with 5 mM AMP-PNP and UMA for 5 hours. plate Liu-S-097, A6. Puck: PSL-1616, Cryo: 2.5M ammonium sulfate |
