7EC3
Crystal structure of SdgB (complexed with UDP, GlcNAc, and Glycosylated peptide)
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 | 47.050 - 2.500 |
R-factor | 0.193 |
Rwork | 0.191 |
R-free | 0.24000 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 7ec1 |
RMSD bond length | 0.008 |
RMSD bond angle | 1.707 |
Data reduction software | HKL-2000 |
Data scaling software | HKL-2000 |
Phasing software | MOLREP |
Refinement software | REFMAC (5.8.0267) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 50.000 | 2.540 |
High resolution limit [Å] | 2.500 | 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 |