7T1D
Human SIRT2 in complex with small molecule 359
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ESRF BEAMLINE MASSIF-1 |
Synchrotron site | ESRF |
Beamline | MASSIF-1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2020-09-01 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 1.0332 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 36.775, 55.980, 139.576 |
Unit cell angles | 90.00, 94.46, 90.00 |
Refinement procedure
Resolution | 35.002 - 1.750 |
Rwork | 0.163 |
R-free | 0.21280 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | CRELUX reference structure of SIRT2 |
RMSD bond length | 0.010 |
RMSD bond angle | 1.574 |
Data reduction software | XDS |
Data scaling software | Aimless (0.7.4) |
Phasing software | PHASER |
Refinement software | REFMAC (5.8.0267) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 139.150 | 139.150 | 1.780 |
High resolution limit [Å] | 1.750 | 9.090 | 1.750 |
Rmerge | 0.075 | 0.040 | 0.612 |
Rmeas | 0.089 | 0.048 | 0.727 |
Rpim | 0.047 | 0.025 | 0.388 |
Total number of observations | 194963 | 1502 | 10269 |
Number of reflections | 56312 | 443 | 3005 |
<I/σ(I)> | 9.5 | 26.7 | 1.9 |
Completeness [%] | 98.6 | 99.6 | 98.9 |
Redundancy | 3.5 | 3.4 | 3.4 |
CC(1/2) | 0.996 | 0.992 | 0.664 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 293.15 | Crystals of SIRT2 in complex with FLS-359 were obtained using hanging-drop vapour diffusion setups. SIRT2 at a concentration of 21.9 mg/ml (50 mM Hepes-NaOH, 150 mM NaCl, pH 8.0) was preincubated with 3.6 mM (5.7-fold molar excess) of FLS-359 (100 mM in DMSO) for 1 h. 1 ul of the protein solution was then mixed with 2 ul of reservoir solution (0.1 M Hepes-NaOH pH 6.6, 0.3 M Li2SO4, 21 % (w/v) PEG 3350) and streak seeded before being equilibrated at 20C over 0.2 ml of reservoir solution. Well diffracting crystals grew as thick aggregates of thin plates and were mounted within 19 days |