6VXE

Crystal structure of hydroxyproline dehydratase (HypD) from Clostridioides difficile with substrate trans-4-hydroxy-L-proline bound

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 24-ID-E
Synchrotron site	APS
Beamline	24-ID-E
Temperature [K]	100
Detector technology	PIXEL
Collection date	2016-04-08
Detector	DECTRIS PILATUS 6M
Wavelength(s)	0.9795
Spacegroup name	P 1 21 1
Unit cell lengths	100.346, 341.655, 122.605
Unit cell angles	90.00, 107.14, 90.00

Refinement procedure

Resolution	49.295 - 2.464
R-factor	0.1962
Rwork	0.195
R-free	0.22960
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5fau
RMSD bond length	0.012
RMSD bond angle	1.243
Data reduction software	XDS
Data scaling software	XDS
Phasing software	PHASER
Refinement software	PHENIX (1.16_3549)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	50.000	2.590
High resolution limit [Å]	2.464	2.520
Number of reflections	278476	44812
<I/σ(I)>	10.75	2.12
Completeness [%]	99.7	99.4
Redundancy	6.98
CC(1/2)	0.994	0.721

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	14% (w/v) polyethylene glycol (PEG) 3350, 100 mM potassium chloride, 100 mM HEPES pH 7.5, 4 mM trans-4-hydroxy-L-proline. Cryoprotectant contained 25% (v/v) dimethyl sulfoxide (DMSO)