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 |