8AYF

Crystal structure of human Sphingosine-1-phosphate lyase 1

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	ELETTRA BEAMLINE 5.2R
Synchrotron site	ELETTRA
Beamline	5.2R
Temperature [K]	100
Detector technology	PIXEL
Collection date	2022-02-10
Detector	DECTRIS PILATUS 6M
Wavelength(s)	1.0000
Spacegroup name	P 1 21 1
Unit cell lengths	59.160, 127.410, 66.950
Unit cell angles	90.00, 104.85, 90.00

Refinement procedure

Resolution	57.760 - 1.840
R-factor	0.192
Rwork	0.191
R-free	0.21450
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	4q6r
RMSD bond length	0.008
RMSD bond angle	1.408
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	MOLREP
Refinement software	REFMAC (5.8.0352)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	57.760	2.090
High resolution limit [Å]	1.840	1.840
Number of reflections	47604	2380
<I/σ(I)>	7.8	1.7
Completeness [%]	92.6	67.4
Redundancy	6.2	6.1
CC(1/2)	0.990	0.421

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	6.5	294	Protein solution: hSPL 108uM in Tris-HCl 20 mM pH 8.0 NaCl 150 mM DTT 1mM Glycerol 5% Precipitant: (Hit G4 of Molecular Dimension screen Morpheus) 0.02M Sodium formate; 0.02M Ammonium acetate; 0.02M Sodium citrate tribasic dihydrate; 0.02M Potassium sodium tartrate tetrahydrate; 0.02M Sodium oxamate; Imidazole 0.05M; MES monohydrate (acid) 0.05M; 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350 mixing volumes: 0.3 + 0.3 uL