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 |