9YD8

Crystal structure of Phospholipase D (PLD) from Arcanobacterium haemolyticum

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	LNLS SIRIUS BEAMLINE MANACA
Synchrotron site	LNLS SIRIUS
Beamline	MANACA
Temperature [K]	100
Detector technology	PIXEL
Collection date	2025-01-25
Detector	DECTRIS PILATUS 2M
Wavelength(s)	1.459
Spacegroup name	P 21 21 2
Unit cell lengths	94.289, 96.704, 61.731
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	67.510 - 2.450
R-factor	0.2326
Rwork	0.229
R-free	0.29900
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.010
RMSD bond angle	1.162
Data reduction software	XDS
Data scaling software	XDS
Phasing software	REFMAC
Refinement software	PHENIX ((1.20.1_4487: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	67.510	2.560
High resolution limit [Å]	2.450	2.450
Number of reflections	40045	5001
<I/σ(I)>	7.3
Completeness [%]	99.8
Redundancy	6.9
CC(1/2)	0.997	0.275

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	0.01 M nickel(II) chloride hexahydrate, 0.1 M Tris pH 7.5, and 20% w/v polyethylene glycol monomethyl ether 2,000