9BN9

Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli in complex with UMA and two inhibitor A19 molecules

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	65.381, 65.381, 134.681
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	58.820 - 1.230
R-factor	0.1242
Rwork	0.123
R-free	0.14240
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.006
RMSD bond angle	0.926
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]	67.340	1.260
High resolution limit [Å]	1.230	1.230
Rmerge	0.048	0.756
Rmeas	0.050	0.854
Rpim	0.014	0.387
Total number of observations	1877914	42363
Number of reflections	159202	9248
<I/σ(I)>	22.8	1.7
Completeness [%]	97.6
Redundancy	11.8	4.6
CC(1/2)	1.000	0.646

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-0407, Cryo: 2.5M Lithium Sulfate + 2mM inhibitor A19