7PR8
Crystal structure of human heparanase in complex with covalent inhibitor GR109
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 | 46.490, 71.290, 79.070 |
Unit cell angles | 90.00, 95.20, 90.00 |
Refinement procedure
Resolution | 39.370 - 1.660 |
Rwork | 0.167 |
R-free | 0.19430 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5e8m |
RMSD bond length | 0.010 |
RMSD bond angle | 1.694 |
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] | 39.370 | 1.700 |
High resolution limit [Å] | 1.660 | 1.660 |
Rmerge | 0.052 | 1.415 |
Rpim | 0.029 | 0.789 |
Number of reflections | 59928 | 4353 |
<I/σ(I)> | 12.5 | 1 |
Completeness [%] | 98.6 | |
Redundancy | 4.2 | |
CC(1/2) | 0.999 | 0.532 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 0.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG3350 |