7MY9

Structure of proline utilization A with 1,3-dithiolane-2-carboxylate bound in the proline dehydrogenase active site

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 24-ID-C
Synchrotron site	APS
Beamline	24-ID-C
Temperature [K]	100
Detector technology	PIXEL
Collection date	2019-11-02
Detector	DECTRIS PILATUS 6M-F
Wavelength(s)	0.979100
Spacegroup name	P 1 21 1
Unit cell lengths	101.932, 103.094, 126.906
Unit cell angles	90.00, 106.50, 90.00

Refinement procedure

Resolution	121.682 - 1.628
R-factor	0.1637
Rwork	0.162
R-free	0.19210
Structure solution method	FOURIER SYNTHESIS
Starting model (for MR)	5kf6
Data reduction software	XDS
Data scaling software	Aimless (0.5.32)
Phasing software	PHENIX
Refinement software	PHENIX (1.14)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	121.682	121.680	1.660
High resolution limit [Å]	1.628	8.920	1.630
Rmerge	0.053	0.020	0.723
Rmeas	0.061	0.023	0.851
Rpim	0.031	0.011	0.441
Total number of observations		7889	50183
Number of reflections	309107	1984	14533
<I/σ(I)>	14.5	50.4	1.5
Completeness [%]	98.5	97.9	93.7
Redundancy	3.8	4	3.5
CC(1/2)	0.999	0.999	0.628

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8	286	Protein stock solution: 6 mg/mL PutA with 50 mM 1,3-dithiolane-2-carboxylate in a buffer containing 50 mM Tris (pH 8.0), 50 mM NaCl, 5% (w/v) glycerol, and 0.5 mM Tris(2-caboxyethyl)phosphine. Reservoir solution: 19 % PEG-3350, 0.2 M ammonium sulfate, 0.1 M magnesium chloride, 0.1 M HEPES (pH 8.0), and 0.1 M sodium formate. Cryo-buffer: reservoir supplemented with 15 % PEG-200. Crystals were grown and harvested in low-light conditions