8V8X

Crystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli (Orthorhombic P form2)

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 21 21 21
Unit cell lengths	57.796, 63.192, 119.988
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	42.650 - 2.300
R-factor	0.2153
Rwork	0.213
R-free	0.25710
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.002
RMSD bond angle	0.475
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]	43.510	2.380
High resolution limit [Å]	2.300	2.300
Rmerge	0.153	0.983
Rmeas	0.167	1.061
Rpim	0.064	0.396
Total number of observations	134921	13766
Number of reflections	20187	1952
<I/σ(I)>	8.2	1.9
Completeness [%]	99.9
Redundancy	6.7	7.1
CC(1/2)	0.992	0.777

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	Morpheus H4: 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 DL-Glutamic acid, 20 mM DL-Alanine; 20 mM Glycine, 20 mM DL-Lysine monohydrochloride and 20 mM DL-Serine. EscoA.17938.a.AE1.PW39153 at 17.4 mg/mL. Inhibitor added but not bound. plate 13512 well H4 drop 2. Puck: PSL-1715, Cryo: direct