8CM8
Galectin-8 N-terminal carbohydrate recognition domain in complex with 4-(bromophenyl)phthalazinone D-galactal ligand
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I24 |
Synchrotron site | Diamond |
Beamline | I24 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-09-18 |
Detector | DECTRIS PILATUS3 X 6M |
Wavelength(s) | 0.99990 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 54.710, 62.280, 84.750 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 50.186 - 1.220 |
R-factor | 0.17119 |
Rwork | 0.169 |
R-free | 0.21391 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.015 |
RMSD bond angle | 1.914 |
Data reduction software | xia2 (0.3.6.3) |
Data scaling software | Aimless (0.7.7) |
Phasing software | PHASER (2.7.14) |
Refinement software | REFMAC (5.8.0403) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 50.190 | 1.252 |
High resolution limit [Å] | 1.220 | 1.220 |
Rmerge | 0.076 | 0.050 |
Rmeas | 0.079 | 0.054 |
Rpim | 0.023 | 0.022 |
Number of reflections | 82202 | 6317 |
<I/σ(I)> | 13.5 | |
Completeness [%] | 99.9 | 99.9 |
Redundancy | 11.9 | 9 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 293.5 | A co-crystal with lactose, grown from 12 mg/ml galectin-8N in 10 mM lactose, 10 mM Tris/HCl pH 8.0, 1 mM TCEP and 150 mM sodium chloride mixed with 25% (w/v) PEG 2000 MME) in a hanging drop, was used to soak the compound by transferring crystals in three steps to soaking drops. These were 2 uL drops with a soaking solution of 20% ethylene glycol, 25% PEG 2000 MME, 10 mM Tris pH 8, 1 mM TCEP, 50 mM NaCl, and 2 mM compound 10. The incubation times in the first two drops were about 10 min and in the third drop about 24 h. Then the crystals were transferred to a cryo solution with the same constituents and flash-frozen in liquid nitrogen. |