6VXC

Crystal structure of hydroxyproline dehydratase (HypD) from Clostridioides difficile

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	2015-06-22
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	49.817 - 2.050
R-factor	0.1685
Rwork	0.167
R-free	0.19490
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5fau
RMSD bond length	0.007
RMSD bond angle	0.956
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	2.090
High resolution limit [Å]	2.048	2.050
Number of reflections	486251	24062
<I/σ(I)>	8.4	1.82
Completeness [%]	99.0	98.3
Redundancy	7.07	7.01
CC(1/2)	0.990	0.588

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, and 100 mM HEPES pH 7.5. Cryoprotectant contained 15% (v/v) glycerol