8VW2

Crystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli (ATP bound)

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	2023-12-09
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9785
Spacegroup name	P 21 21 21
Unit cell lengths	58.456, 69.944, 100.534
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	44.850 - 1.950
R-factor	0.1723
Rwork	0.170
R-free	0.22490
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.008
RMSD bond angle	0.934
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX ((1.21_5219: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	44.850	2.000
High resolution limit [Å]	1.950	1.950
Rmerge	0.125	1.151
Rmeas	0.133	1.230
Rpim	0.046	0.428
Total number of observations	240573	16660
Number of reflections	30773	2139
<I/σ(I)>	10.7	1.7
Completeness [%]	99.9
Redundancy	7.8	7.8
CC(1/2)	0.998	0.826

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	Morpheus A8: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM HEPES/MOPS, pH 7.5, 30 mM MgCl2 and 30 mM CaCl2, 2% (v/v) DMSO. EscoA.17938.a.AE1.PW39153 at 17.4 mg/mL. 4 hour soak in 5 mM ATP. plate 13768 well E4 drop 1 or 2. Puck: PSL-1106, Cryo: direct