8VW1

Crystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli (ADP 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	58.470, 69.235, 100.468
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	40.820 - 1.700
R-factor	0.1644
Rwork	0.163
R-free	0.19670
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.009
RMSD bond angle	1.047
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]	44.670	1.730
High resolution limit [Å]	1.700	1.700
Rmerge	0.096	1.874
Rmeas	0.100	1.945
Rpim	0.028	0.519
Total number of observations	600089	32440
Number of reflections	45584	2371
<I/σ(I)>	15	1.6
Completeness [%]	99.9
Redundancy	13.2	13.7
CC(1/2)	0.999	0.723

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 ADP. plate 13768 well E4 drop 1 or 2. Puck: PSL-1105, Cryo: direct