9DL6

Structure of proline utilization A complexed with piperidine-3-carboxylic acid

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	ALS BEAMLINE 8.2.1
Synchrotron site	ALS
Beamline	8.2.1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-04-25
Detector	DECTRIS EIGER2 S 9M
Wavelength(s)	1.00002
Spacegroup name	P 1 21 1
Unit cell lengths	100.514, 101.828, 126.545
Unit cell angles	90.00, 106.43, 90.00

Refinement procedure

Resolution	45.850 - 1.420
R-factor	0.1685
Rwork	0.167
R-free	0.18890
Structure solution method	FOURIER SYNTHESIS
RMSD bond length	0.006
RMSD bond angle	0.882
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX (1.21rc1_5156)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	48.210	1.440
High resolution limit [Å]	1.420	1.420
Rmerge	0.051	1.538
Rmeas	0.056	1.733
Rpim	0.021	0.785
Total number of observations		58042
Number of reflections	822821	12404
<I/σ(I)>	18.1	0.8
Completeness [%]	91.4
Redundancy	6.7	4.7
CC(1/2)	0.999	0.335

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		293	Reservoir contained 0.1 M HEPES, pH 7.5, 0.1 M sodium formate, 0.1 M magnesium chloride, 0.15 M ammonium sulfate, and 18% (w/v) PEG 3350. Enzyme was incubated with 20 mM piperidine-3-carboxylic acid and 5 mM NAD+. Crystal was soaked in cryobuffer containing 73 mM piperidine-3-carboxylic acid and 20% PEG 200