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