9OZO

Structure of phospholipase D BetaIB1i from Sicarius terrosus venom, H47N mutant bound to product and substrate sphingolipids at 2.2 A resolution from a 2-day old crystal

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	LIQUID ANODE
Source details	BRUKER METALJET
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-12-20
Detector	Bruker PHOTON III
Wavelength(s)	1.34138
Spacegroup name	I 1 2 1
Unit cell lengths	79.815, 105.140, 108.095
Unit cell angles	90.00, 93.68, 90.00

Refinement procedure

Resolution	24.430 - 2.200
R-factor	0.15429
Rwork	0.152
R-free	0.19916
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.007
RMSD bond angle	1.594
Data reduction software	PROTEUM2
Data scaling software	Aimless
Phasing software	MOLREP
Refinement software	REFMAC (5.8.0425)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	24.430	2.270
High resolution limit [Å]	2.200	2.200
Rmerge	0.160	0.662
Number of reflections	45116	3884
<I/σ(I)>	7.1	1.5
Completeness [%]	99.8	99.4
Redundancy	4.9	2.7
CC(1/2)	0.981	0.425

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP		298	1 mg/mL protein, 0.4 mM ceramidephosphoethanolamine, 5 mg/mL CHAPS, 8.25% methyl-2,4-pentanediol, 75 mM sodium chloride, 27.5 mM sodium acetate (pH 4.6), ~30 mM Tris, 1 mM magnesium chloride