7YM0

Lysoplasmalogen-specific phospholipase D (LyPls-PLD) with Ca2+

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	PHOTON FACTORY BEAMLINE BL-1A
Synchrotron site	Photon Factory
Beamline	BL-1A
Temperature [K]	100
Detector technology	PIXEL
Collection date	2020-02-26
Detector	DECTRIS EIGER X 4M
Wavelength(s)	1.08
Spacegroup name	P 43 21 2
Unit cell lengths	142.952, 142.952, 126.134
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	47.290 - 2.910
R-factor	0.1788
Rwork	0.177
R-free	0.21450
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.007
RMSD bond angle	0.840
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	MOLREP
Refinement software	PHENIX ((1.14_3260: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	47.650	3.090
High resolution limit [Å]	2.910	2.910
Rmeas	0.111
Number of reflections	29314	4656
<I/σ(I)>	16.1	2.6
Completeness [%]	100.0
Redundancy	14.3
CC(1/2)	0.999	0.879

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	EVAPORATION	9.5	293	0.1 M Ches pH 9.5, 50 mM NaCl, and 12% PEG3350