8RIP

Beta-keto acid cleavage enzyme from Paracoccus denitrificans with bound malonate and Coenzyme A

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)
Synchrotron site	PETRA III, EMBL c/o DESY
Beamline	P14 (MX2)
Temperature [K]	100
Detector technology	PIXEL
Collection date	2021-08-20
Detector	DECTRIS EIGER2 X CdTe 16M
Wavelength(s)	0.9763
Spacegroup name	P 21 21 21
Unit cell lengths	79.155, 134.350, 140.848
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	29.990 - 1.810
R-factor	0.1579
Rwork	0.158
R-free	0.17800
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.007
RMSD bond angle	0.876
Data reduction software	XDS (20210323)
Data scaling software	SCALA (3.3.22)
Phasing software	PHENIX (1.20.1_4487)
Refinement software	PHENIX (1.20.1_4487)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	29.990	1.910
High resolution limit [Å]	1.810	1.810
Rmerge	0.069	0.908
Rmeas	0.073	0.962
Rpim	0.024	0.313
Total number of observations	1245111	180122
Number of reflections	136868	19659
<I/σ(I)>	18.4	2.3
Completeness [%]	99.8
Redundancy	9.1	9.2
CC(1/2)	0.999	0.811

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7	289	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 20 % w/v PEG3350, 200 mM di-sodium malonate pH 7.0. The final size of the drops was 1 microliter. Prior to flash freezing the crystal in liquid nitrogen, the mother liquor was supplemented with 10 mM CoA and 40 % (w/v) PEG200.