5J3S
Crystal structure of the catalytic domain of human tyrosyl DNA phosphodiesterase 2 in complex with a small molecule inhibitor
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | DIAMOND BEAMLINE I04 |
| Synchrotron site | Diamond |
| Beamline | I04 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2013-02-24 |
| Detector | DECTRIS PILATUS 6M-F |
| Wavelength(s) | 0.9795 |
| Spacegroup name | P 65 2 2 |
| Unit cell lengths | 68.516, 68.516, 209.505 |
| Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
| Resolution | 45.218 - 3.400 |
| R-factor | 0.2549 |
| Rwork | 0.254 |
| R-free | 0.27290 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 5j3p |
| RMSD bond length | 0.002 |
| RMSD bond angle | 0.494 |
| Data reduction software | XDS |
| Data scaling software | Aimless |
| Phasing software | PHASER |
| Refinement software | PHENIX ((1.10.1_2155: ???)) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 45.220 | 3.670 |
| High resolution limit [Å] | 3.400 | 3.400 |
| Rmerge | 0.242 | 2.025 |
| Number of reflections | 7545 | |
| <I/σ(I)> | 6.4 | 1.1 |
| Completeness [%] | 99.9 | 100 |
| Redundancy | 6.3 | 6.8 |
| CC(1/2) | 0.990 | 0.540 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 273 | 1.2M D/L-Malic acid pH7.0, 0.1M Bis-Tris propane pH 7.0, 3% v/v DMSO |
