6Z8W
X-ray structure of the complex between human alpha thrombin and a thrombin binding aptamer variant (TBA-3G), which contains 1-beta-D-glucopyranosyl residue in the side chain of Thy3 at N3.
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 | 2019-12-02 |
Detector | DECTRIS EIGER2 XE 16M |
Wavelength(s) | 0.9795 |
Spacegroup name | P 32 2 1 |
Unit cell lengths | 94.798, 94.798, 125.326 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 82.100 - 1.730 |
R-factor | 0.1795 |
Rwork | 0.178 |
R-free | 0.20720 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1ppb |
RMSD bond length | 0.016 |
RMSD bond angle | 2.304 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | REFMAC (5.8.0258) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 125.330 | 1.940 |
High resolution limit [Å] | 1.730 | 1.730 |
Number of reflections | 41910 | 2097 |
<I/σ(I)> | 19 | 1.9 |
Completeness [%] | 94.4 | 72 |
Redundancy | 20.1 | 15.6 |
CC(1/2) | 1.000 | 0.700 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 200 mM KCl, 35% v/v pentaerythritol propoxylate, 50 mM HEPES, pH 7.5 |