8V8W
Crystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli (Tetragonal P form)
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 | 2023-10-08 |
Detector | DECTRIS EIGER2 XE 9M |
Wavelength(s) | 0.9795 |
Spacegroup name | P 43 21 2 |
Unit cell lengths | 67.801, 67.801, 200.023 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 47.540 - 1.650 |
R-factor | 0.1796 |
Rwork | 0.179 |
R-free | 0.19800 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.009 |
RMSD bond angle | 0.978 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | PHENIX ((1.21rc1_5162: ???)) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 47.940 | 1.680 |
High resolution limit [Å] | 1.650 | 1.650 |
Rmerge | 0.088 | 1.582 |
Rmeas | 0.092 | 1.644 |
Rpim | 0.026 | 0.444 |
Total number of observations | 740487 | 37493 |
Number of reflections | 57294 | 2762 |
<I/σ(I)> | 13.8 | 1.7 |
Completeness [%] | 100.0 | |
Redundancy | 12.9 | 13.6 |
CC(1/2) | 0.999 | 0.808 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 291 | Morpheus G4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 20 mM Sodium formate, 20 mM Ammonium acetate, 20 mM Sodium citrate tribasic, 20 mM Potassium sodium tartrate and 20 mM Sodium oxamate. EscoA.17938.a.AE1.PW39153 at 17.4 mg/mL. Inhibitor added but not bound. plate 13512 well G4 drop 1. Puck: PSL-1712, Cryo: direct |