5EBB

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

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
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

Crystal Properties
Matthews coefficient	Solvent content
3.15	56.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 147.79	α = 90
b = 147.79	β = 90
c = 139.9	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS PILATUS 2M		2015-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9174	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.6	48.46	99.5	0.132	9.8	5.7	61111	54349

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.68	99.9		0.561	2.9	5.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.6	48.38	51505	2760	99.33	0.23803	0.23712	0.25474	RANDOM	21.786

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.15	-0.07		-0.15		0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.22
r_dihedral_angle_4_deg	18.141
r_dihedral_angle_3_deg	18.035
r_dihedral_angle_1_deg	7.465
r_long_range_B_refined	5.736
r_long_range_B_other	5.736
r_scangle_other	3.932
r_mcangle_it	3.025
r_mcangle_other	3.024
r_scbond_it	2.452
r_scbond_other	2.452
r_angle_refined_deg	2.124
r_angle_other_deg	2.1
r_mcbond_it	1.865
r_mcbond_other	1.865
r_chiral_restr	0.117
r_bond_refined_d	0.022
r_gen_planes_refined	0.011
r_gen_planes_other	0.009
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9864
Nucleic Acid Atoms
Solvent Atoms	301
Heterogen Atoms	165

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
autoSHARP	phasing
Aimless	data scaling
Coot	model building
ARP	model building