5VYB
Structure of the carbohydrate recognition domain of Dectin-2 complexed with a mammalian-type high mannose Man9GlcNAc2 oligosaccharide
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SSRL BEAMLINE BL12-2 |
Synchrotron site | SSRL |
Beamline | BL12-2 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2017-03-18 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.97946 |
Spacegroup name | C 2 2 21 |
Unit cell lengths | 64.055, 78.834, 76.459 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 38.229 - 2.400 |
R-factor | 0.2069 |
Rwork | 0.205 |
R-free | 0.24040 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4zrv |
RMSD bond length | 0.007 |
RMSD bond angle | 0.528 |
Data reduction software | XDS |
Data scaling software | Aimless (0.5.31) |
Phasing software | PHASER |
Refinement software | PHENIX |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 38.230 | 38.230 | 2.480 |
High resolution limit [Å] | 2.390 | 8.950 | 2.390 |
Rmerge | 0.080 | 0.049 | 0.432 |
Rmeas | 0.088 | 0.057 | 0.482 |
Rpim | 0.038 | 0.029 | 0.207 |
Number of reflections | 7880 | ||
<I/σ(I)> | 12.4 | ||
Completeness [%] | 99.4 | 97.3 | 97.3 |
Redundancy | 5.2 | 4.3 | 5.1 |
CC(1/2) | 0.990 | 0.908 | 0.931 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 295 | Drop size: 0.9:0.9 micro-liter of protein:reservoir protein solution: 2 mg/ml CRD, 5 mM CaCl2, 10 mM Tris-Cl, pH 8.0, 25 mM NaCl, and 2 mM Man9GlcNAc2. The reservoir solution: 1.0 M NaCl, 6% polyethylene glycol 400 and 0.1 M Tris-Cl, pH 8.0. freezing solution: 30% polyethylene glycol 400, 1.0 M NaCl, 0.1 M Tris-Cl, pH 8.0, and 2 mM Man9GlcNAc2. |