7U35
Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from Pseudomonas aeruginosa PAO1 in complex with ADP
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 21-ID-F |
Synchrotron site | APS |
Beamline | 21-ID-F |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2022-02-17 |
Detector | RAYONIX MX-300 |
Wavelength(s) | 0.97872 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 68.190, 131.180, 79.540 |
Unit cell angles | 90.00, 106.93, 90.00 |
Refinement procedure
Resolution | 37.910 - 1.950 |
R-factor | 0.1713 |
Rwork | 0.171 |
R-free | 0.20450 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | apo structure pdb entry 7SY9 in two domains |
RMSD bond length | 0.007 |
RMSD bond angle | 0.850 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER |
Refinement software | PHENIX (1.20-4438) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 2.000 |
High resolution limit [Å] | 1.950 | 8.720 | 1.950 |
Rmerge | 0.044 | 0.027 | 0.314 |
Rmeas | 0.049 | 0.030 | 0.353 |
Number of reflections | 95481 | 1059 | 6920 |
<I/σ(I)> | 21.07 | 46.91 | 4.28 |
Completeness [%] | 98.2 | 94.1 | 96.4 |
Redundancy | 5.111 | 4.823 | 4.704 |
CC(1/2) | 0.999 | 0.999 | 0.931 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.55 | 287 | Optimization condition around RigakuReagents JCSG Top96 B6: 21% (w/V) PEG 3350, 100mM HEPES/NaOH pH 7.55: PsaeA.17938.a.B2.PW38065 at 40mg/ml + 5mM ADP + 5mM MgCl2. Tray: 324078 e4: cryo: 20% EG + compounds in 2 steps: puck ECC9-7. |