7TXR
Crystal structure of the Vitronectin hemopexin-like domain binding Calcium-2
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SSRL BEAMLINE BL9-2 |
Synchrotron site | SSRL |
Beamline | BL9-2 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-05-17 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.97946 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 40.835, 98.277, 49.433 |
Unit cell angles | 90.00, 99.82, 90.00 |
Refinement procedure
Resolution | 37.240 - 2.000 |
R-factor | 0.1867 |
Rwork | 0.184 |
R-free | 0.22590 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6o5e |
RMSD bond length | 0.008 |
RMSD bond angle | 1.395 |
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] | 37.240 | 2.050 |
High resolution limit [Å] | 2.000 | 2.000 |
Rmerge | 0.112 | 0.510 |
Number of reflections | 23919 | 1104 |
<I/σ(I)> | 5.6 | |
Completeness [%] | 92.0 | 57.6 |
Redundancy | 3.3 | 2.6 |
CC(1/2) | 0.840 | 0.720 |
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 CaCl2, 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. |