5U62
Crystal structure of EED in complex with H3K27Me3 peptide and 6-(benzo[d][1,3]dioxol-4-ylmethyl)-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | ROTATING ANODE |
Source details | RIGAKU FR-E+ SUPERBRIGHT |
Temperature [K] | 270 |
Detector technology | IMAGE PLATE |
Collection date | 2016-06-22 |
Detector | RIGAKU RAXIS IV++ |
Wavelength(s) | 1.5418 |
Spacegroup name | P 21 21 2 |
Unit cell lengths | 92.881, 178.113, 50.480 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 44.940 - 1.900 |
R-factor | 0.17 |
Rwork | 0.168 |
R-free | 0.20800 |
RMSD bond length | 0.010 |
RMSD bond angle | 1.090 |
Data reduction software | XDS |
Data scaling software | SCALA |
Phasing software | AMoRE |
Refinement software | BUSTER (2.10.2) |
Data quality characteristics
Overall | |
Low resolution limit [Å] | 46.440 |
High resolution limit [Å] | 1.900 |
Number of reflections | 65168 |
<I/σ(I)> | 12.4 |
Completeness [%] | 97.3 |
Redundancy | 5.7 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 291 | Using a PEG/salt combination as a precipitant. Briefly, EED was incubated with 10 mM B-nicotinamide adenine dinucleotide hydrate, 2 mM of a tightly binding proprietary compound, and 0.5 mM of a synthesized peptide which comprises the helix on EZH2 which interacts with EED. The crystals were grown using the vapor diffusion method. One uL of the protein mixture was combined with 1 uL of a precipitant comprised of 20% (w/v) PEG3350, 0.2 M potassium iodide, and 0.1M Tris-HCl, pH 8.5, on a cover slip which was suspended over a reservoir comprised of 0.5 mL of precipitant at 18 Celsius and sealed. The crystals grew in 4-6 days at 18 Celsius and then harvested and soaked in defined drops consisting of 30 uL of precipitant and 2 mM of compound for 24 h. Crystals were cryopreserved for data collection using a cryosolution consisting of 30% PEG 400 (v/v), 20% (w/v) PEG 3350, 0.2 M potassium iodide, and 0.1M Tris-HCl, pH 8.5. |