7AFV
Crystal structure of tetrameric beta-2-microglobulin deltaN6 S52C stabilized by a covalent ligand
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I24 |
Synchrotron site | Diamond |
Beamline | I24 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2020-02-03 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 0.9795 |
Spacegroup name | P 43 21 2 |
Unit cell lengths | 87.572, 87.572, 56.458 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 61.920 - 2.400 |
R-factor | 0.2361 |
Rwork | 0.233 |
R-free | 0.28840 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2yxf |
RMSD bond length | 0.007 |
RMSD bond angle | 1.553 |
Data reduction software | XSCALE |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | REFMAC (5.8.0258) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 61.920 | 2.530 |
High resolution limit [Å] | 2.400 | 2.400 |
Rmerge | 1.913 | |
Number of reflections | 8519 | 8519 |
<I/σ(I)> | 9.8 | |
Completeness [%] | 100.0 | |
Redundancy | 23 | |
CC(1/2) | 0.999 | 0.789 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293 | Drop protein volume 0.2 uL Drop well volume 0.1 uL 0.04 M Porpheus Alcohol Mix (Complex ingredient) 0.1 M Morpheus Buffer System 3 pH 8.5 (Buffer) 31 %w/v Morpheus Precipitant Mix 4 (Precipitant) Stock Solutions: Porpheus Alcohol Mix 0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol (for a final concentration of 6.7 mM of 1,6-hexanediol, 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol) Morpheus Buffer System 3 pH 8.5 1M Tris and 1M BICINE (for a final concentration of 39.1 mM Bicine pH = 5.03 and 60.9 M Tris pH = 10.83) Morpheus Precipitant Mix 25% w/v PEG 3350, 25% w/v PEG 1000, 25% v/v MPD (for a final concentration of 7.75% w/v PEG 1000, 7.75% w/v PEG 3350 and 7.75% v/v MPD) |