7VFL

Crystal structure of SdgB (UDP, NAG, and O-glycosylated SD peptide-binding form)

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	PHOTON FACTORY BEAMLINE BL-1A
Synchrotron site	Photon Factory
Beamline	BL-1A
Temperature [K]	100
Detector technology	PIXEL
Collection date	2015-05-20
Detector	DECTRIS EIGER X 4M
Wavelength(s)	1.1000
Spacegroup name	P 21 21 21
Unit cell lengths	70.201, 130.568, 189.854
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	47.000 - 2.450
R-factor	0.185
Rwork	0.182
R-free	0.24000
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	7ec1
Data reduction software	HKL-2000
Data scaling software	HKL-2000
Phasing software	MOLREP
Refinement software	PHENIX (1.19.2_4158)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	50.000	2.540
High resolution limit [Å]	2.450	2.500
Number of reflections	60708	2941
<I/σ(I)>	12.9
Completeness [%]	96.7
Redundancy	5.4
CC(1/2)	0.934	0.776

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		287	20 mM CaCl2, 85 mM tri-sodium citrate at pH 5.6, 25.5% (w/v) PEG 4,000, and 15% (w/v) glycerol for the SdgB crystal soaked with the 2.66 mM 9mer SD-repeat peptide and 9.60 mM UDP-GlcNAc