8B0C
Crystal structure of human heparanase in complex with covalent inhibitor VB158
This is a non-PDB format compatible entry.
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 | 2021-07-04 |
Detector | DECTRIS EIGER2 X 16M |
Wavelength(s) | 0.9762 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 45.976, 71.441, 78.261 |
Unit cell angles | 90.00, 95.45, 90.00 |
Refinement procedure
Resolution | 52.710 - 2.100 |
Rwork | 0.202 |
R-free | 0.26210 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5e8m |
RMSD bond length | 0.009 |
RMSD bond angle | 1.668 |
Data reduction software | DIALS |
Data scaling software | DIALS |
Phasing software | PHASER |
Refinement software | REFMAC (5.8.0258) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 52.710 | 2.160 |
High resolution limit [Å] | 2.100 | 2.100 |
Number of reflections | 29584 | 2411 |
<I/σ(I)> | 8.3 | 0.8 |
Completeness [%] | 100.0 | |
Redundancy | 5.7 | |
CC(1/2) | 0.998 | 0.592 |
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 |