8DP2

Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from Pseudomonas aeruginosa PAO1 in complex with UMA (Uridine-5'-diphosphate-N-acetylmuramoyl-L-Alanine)

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 21-ID-F
Synchrotron site	APS
Beamline	21-ID-F
Temperature [K]	100
Detector technology	CCD
Collection date	2022-06-09
Detector	RAYONIX MX-300
Wavelength(s)	0.97872
Spacegroup name	P 61
Unit cell lengths	95.460, 95.460, 99.550
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	41.340 - 1.600
R-factor	0.1506
Rwork	0.150
R-free	0.16890
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	ADP-bound MurD pdb entry 7U35 in three domains
RMSD bond length	0.009
RMSD bond angle	1.048
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	PHASER
Refinement software	PHENIX (1.20.1)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	1.640
High resolution limit [Å]	1.600	7.160	1.600
Rmerge	0.056	0.032	0.593
Rmeas	0.060	0.034	0.653
Number of reflections	67812	793	5005
<I/σ(I)>	20.91	48.6	2.31
Completeness [%]	100.0	99.4	100
Redundancy	8.964	8.828	5.831
CC(1/2)	0.999	0.999	0.809

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7.5	287	RigakuReagents JCSG Top96 screen, condition b1: 100mM HEPES free acid / sodium hydroxide pH 7.5, 30% (V/V) PEG 400, 5% (w/V) PEG 3000, 10% (V/V) Glycerol: PsaeA.17938.a.B2.PS38065 at 40mg/ml + 3mM UMA (BSI102034) and MgCl2: tray: 325018b1: cryo: direct, puck: tua1-2. SIN is modeled tenatively based on density only, it was not added to the crystallizaton buffer