7U68
Crystal structure of the Vitronectin hemopexin-like domain binding Sodium-2
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SSRL BEAMLINE BL12-2 |
Synchrotron site | SSRL |
Beamline | BL12-2 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2020-11-27 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.97946 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 40.582, 124.905, 40.778 |
Unit cell angles | 90.00, 119.50, 90.00 |
Refinement procedure
Resolution | 35.520 - 2.000 |
R-factor | 0.1878 |
Rwork | 0.184 |
R-free | 0.24700 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 7txr |
RMSD bond length | 0.007 |
RMSD bond angle | 1.393 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | REFMAC (5.8.0257) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 35.520 | 2.050 |
High resolution limit [Å] | 2.000 | 2.000 |
Rmerge | 0.070 | 0.612 |
Number of reflections | 23279 | 1712 |
<I/σ(I)> | 9.9 | 2 |
Completeness [%] | 97.6 | 94.8 |
Redundancy | 3.5 | 3.3 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 1 UL PROTEIN SOLUTION + 1 UL PRECIPITATE SOLUTION containing 0.09 M IMIDAZOLE/MES, PH 6.5, 27 mM SODIUM NITRATE, 27 mM SODIUM PHOSPHATE, 27 mM AMMONIUM SULFATE, 11.25% V/V MPD, 11.25% W/V PEG1000, 11.25% W/V PEG3350, 3% W/V D- (+)-TREHALOSE. Crystals were soaked with 1 mM EDTA, 5 mM SODIUM SULFATE, 27 mM SODIUM NITRATE, 20 mM BisTris pH 7.0, 11.25% V/V MPD, 11.25% W/V PEG1000, 11.25% W/V PEG3350, 3% W/V D-(+)-TREHALOSE. |