9HNF

Beta-keto acid cleavage enzyme from Paracoccus denitrificans with bound acetoacetate and acetyl-CoA

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
Synchrotron site	PETRA III, EMBL c/o DESY
Beamline	P13 (MX1)
Temperature [K]	100
Detector technology	PIXEL
Collection date	2021-09-23
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.9763
Spacegroup name	C 2 2 21
Unit cell lengths	80.900, 138.480, 136.360
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	27.690 - 2.100
R-factor	0.1759
Rwork	0.175
R-free	0.19200
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.003
RMSD bond angle	0.620
Data reduction software	XDS (20240723)
Data scaling software	Aimless (0.7.9)
Phasing software	PHASER (1.21.2_5419)
Refinement software	PHENIX (1.21.2_5419)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	27.690	2.160
High resolution limit [Å]	2.100	2.100
Rmerge	0.114	0.841
Rmeas	0.119	0.874
Rpim	0.032	0.234
Total number of observations	591673
Number of reflections	44681	3628
<I/σ(I)>	14.4	3.2
Completeness [%]	99.4	99.5
Redundancy	13.2	13.5
CC(1/2)	0.998	0.884

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	7.8	288	The enzyme (8.6 mg/mL) in 50 mM HEPES pH 7.8, 150 mM KCl, 1 M L-proline, and 1 mM ZnCl2 was mixed in a 1:1 ratio with 10 % (v/v) pentaerythritol ethoxylate, 10 % v/v 1-Butanol. The final size of the drops was 1 microliter. Prior to flash freezing the crystals in liquid nitrogen, the mother liquor was supplemented with 15 mM acetyl-CoA, 20 mM acetoacetate, and 20 % (v/v) pentaerythrol propoxylate.