7PR7
Crystal structure of human heparanase in complex with covalent inhibitor VL166
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | DIAMOND BEAMLINE I03 |
| Synchrotron site | Diamond |
| Beamline | I03 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2019-11-30 |
| Detector | DECTRIS EIGER2 XE 16M |
| Wavelength(s) | 0.97933 |
| Spacegroup name | P 1 21 1 |
| Unit cell lengths | 46.400, 71.010, 79.230 |
| Unit cell angles | 90.00, 95.14, 90.00 |
Refinement procedure
| Resolution | 46.256 - 1.520 |
| Rwork | 0.166 |
| R-free | 0.18820 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 5e8m |
| RMSD bond length | 0.012 |
| RMSD bond angle | 1.784 |
| Data reduction software | xia2 |
| Data scaling software | Aimless |
| Phasing software | REFMAC |
| Refinement software | REFMAC (5.8.0267) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 52.780 | 1.560 |
| High resolution limit [Å] | 1.520 | 1.520 |
| Rmerge | 0.051 | 1.341 |
| Rpim | 0.028 | 0.741 |
| Number of reflections | 78665 | 5772 |
| <I/σ(I)> | 12.3 | 1.1 |
| Completeness [%] | 99.9 | 100 |
| Redundancy | 4.1 | 4.1 |
| CC(1/2) | 0.998 | 0.479 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 293 | 0.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG3350 |
