7YMP

Crystal structure of lysoplasmalogen specific phospholipase D

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SPRING-8 BEAMLINE BL32XU
Synchrotron site	SPring-8
Beamline	BL32XU
Temperature [K]	100
Detector technology	PIXEL
Collection date	2020-06-05
Detector	DECTRIS EIGER X 9M
Wavelength(s)	1.00
Spacegroup name	P 1 21 1
Unit cell lengths	112.610, 94.940, 147.350
Unit cell angles	90.00, 90.24, 90.00

Refinement procedure

Resolution	47.470 - 2.570
R-factor	0.2134
Rwork	0.210
R-free	0.27170
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	2pz0
RMSD bond length	0.008
RMSD bond angle	1.022
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	PHASER
Refinement software	PHENIX (1.13_2998)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	48.430	2.730
High resolution limit [Å]	2.570	2.570
Rmeas	0.294
Number of reflections	98412	16137
<I/σ(I)>	5.16
Completeness [%]	99.3
Redundancy	5.2
CC(1/2)	0.977	0.570

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	PEG3350, Na Citrate, Ammonium Acetate