10OH

Structure of Clostridium difficile Toxin B (TcdB) glucosyltransferase in complex with UDP and isofagomine analog 2-4

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSLS-II BEAMLINE 17-ID-1
Synchrotron site	NSLS-II
Beamline	17-ID-1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2025-04-08
Detector	DECTRIS EIGER X 9M
Wavelength(s)	0.91976
Spacegroup name	P 21 21 21
Unit cell lengths	50.996, 118.955, 207.965
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	24.940 - 1.850
R-factor	0.1725
Rwork	0.171
R-free	0.20480
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.006
RMSD bond angle	0.815
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX ((1.21.2_5419: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	25.000	1.870
High resolution limit [Å]	1.850	1.850
Rmerge	0.130	0.780
Rmeas	0.130
Rpim	0.040	0.350
Number of reflections	108973	3604
<I/σ(I)>	9.1	2.93
Completeness [%]	100.0	99.2
Redundancy	1.29	13.1
CC(1/2)	0.990	0.830

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7.4	295	0.2 M Potassium sodium tartrate tetrahydrate and 20% (w/v) Polyethylene glycol 3,350