5EBB

Structure of human sphingomyelinase phosphodiesterase like 3A (SMPDL3A) with Zn2+

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	DIAMOND BEAMLINE I04-1
Synchrotron site	Diamond
Beamline	I04-1
Temperature [K]	80
Detector technology	PIXEL
Collection date	2015-02-11
Detector	DECTRIS PILATUS 2M
Wavelength(s)	0.9174
Spacegroup name	P 32 2 1
Unit cell lengths	147.790, 147.790, 139.900
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	48.380 - 2.600
R-factor	0.23803
Rwork	0.237
R-free	0.25474
Structure solution method	SAD
RMSD bond length	0.022
RMSD bond angle	2.124
Data reduction software	XDS (10.9.5)
Data scaling software	Aimless (0.3.11)
Phasing software	autoSHARP (2.60)
Refinement software	REFMAC (5.8.0073)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	48.460	2.680
High resolution limit [Å]	2.600	2.600
Rmerge	0.132	0.561
Number of reflections	54349
<I/σ(I)>	9.8	2.9
Completeness [%]	99.5	99.9
Redundancy	5.7	5.9

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7.2	298	2.08 M disodium malonate pH 7.2, 0.23 M sodium thiocyanate and 0.01 M TCEP