8DT1

Crystal Structure of a Putative D-beta-hydroxybutyrate dehydrogenase from Burkholderia cenocepacia J2315 in complex with NAD

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	ROTATING ANODE
Source details	RIGAKU FR-E+ SUPERBRIGHT
Temperature [K]	100
Detector technology	PIXEL
Collection date	2022-07-18
Detector	RIGAKU HyPix-6000HE
Wavelength(s)	1.5418
Spacegroup name	P 1
Unit cell lengths	59.910, 65.600, 68.320
Unit cell angles	97.15, 98.38, 107.47

Refinement procedure

Resolution	22.170 - 1.800
R-factor	0.1468
Rwork	0.146
R-free	0.17790
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	apo structure PDB entry 4trr
RMSD bond length	0.008
RMSD bond angle	0.939
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	PHASER
Refinement software	PHENIX (1.20.1)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	1.850
High resolution limit [Å]	1.800	8.050	1.800
Rmerge	0.042	0.032	0.297
Rmeas	0.050	0.038	0.396
Number of reflections	88982	965	6505
<I/σ(I)>	15.91	38.43	2.46
Completeness [%]	99.3	95.6	97.5
Redundancy	3.195	3.209	1.873
CC(1/2)	0.999	0.997	0.891

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	4.5	287	Optimized condition around RigakuReagents JCSG+ screen, condition C6:100mM sodium phosphate dibasic/citric acid pH 4.5: 43% (V/V) PEG 300: BuceA.00010.z.B1.PS01812 at 40mg/ml + 5mM NAD/MgCl2: tray: 325332 H9: cryo: reservoir with 5mM NAD and MgCl2: puck jqn3-2.