7U56

Crystal Structure of D-alanine--D-alanine ligase from Klebsiella pneumoniae subsp. pneumoniae in complex with AMP

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	2022-02-10
Detector	RAYONIX MX-300
Wavelength(s)	0.97872
Spacegroup name	P 21 21 2
Unit cell lengths	95.350, 115.420, 68.480
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	39.130 - 1.850
R-factor	0.1628
Rwork	0.162
R-free	0.19920
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	3i12 as per Morda
RMSD bond length	0.008
RMSD bond angle	0.887
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	MoRDa
Refinement software	PHENIX (1.20.1)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	1.900
High resolution limit [Å]	1.850	8.270	1.850
Rmerge	0.081	0.035	0.646
Rmeas	0.088	0.039	0.706
Number of reflections	65184	825	4750
<I/σ(I)>	16.16	43.64	2.74
Completeness [%]	100.0	98.3	100
Redundancy	6.136	5.218	6.133
CC(1/2)	0.998	0.998	0.815

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	287	Anatrace/Calibre MCSG1 screen, condition B11: 200mM magnesium chloride, 100mM TrisBase / HCl pH 8.5, 20% (w/V) PEG 8000: KlpnC.00137.a.B1.PW38983 at 17mg/ml + 3mM Magensium chloride + 3mM AMP: tray: 322140 B11: cryo: 20% EG, puck: ody5-7