9OZS

Structure of phospholipase D BetaIB1i from Sicarius terrosus venom, H47N mutant bound to substrate sphingolipids at 2.60 A resolution

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	80.789, 105.854, 109.108
Unit cell angles	90.00, 93.62, 90.00

Refinement procedure

Resolution	24.410 - 2.600
R-factor	0.15231
Rwork	0.149
R-free	0.20889
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.008
RMSD bond angle	1.780
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]	24.410	2.720
High resolution limit [Å]	2.600	2.600
Rmerge	0.400	1.170
Number of reflections	28219	3441
<I/σ(I)>	4.1	1.9
Completeness [%]	99.8	100
Redundancy	9	7
CC(1/2)	0.941	0.490

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