8BSB
Vc1313-LBD bound to D-lysine
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ESRF BEAMLINE ID30B |
Synchrotron site | ESRF |
Beamline | ID30B |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-06-18 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 0.9763 |
Spacegroup name | P 1 |
Unit cell lengths | 38.337, 44.927, 56.939 |
Unit cell angles | 75.32, 79.17, 73.69 |
Refinement procedure
Resolution | 36.500 - 1.900 |
R-factor | 0.1895 |
Rwork | 0.189 |
R-free | 0.23280 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | Vc1313-LBD with D-arg |
RMSD bond length | 0.003 |
RMSD bond angle | 0.532 |
Data reduction software | XDS |
Data scaling software | XDS |
Phasing software | PHENIX (1.20rc3_4406) |
Refinement software | PHENIX (1.20rc3_4406) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 36.500 | 1.968 |
High resolution limit [Å] | 1.900 | 1.900 |
Rmerge | 0.095 | 0.882 |
Number of reflections | 26736 | 2676 |
<I/σ(I)> | 7.1 | |
Completeness [%] | 96.9 | |
Redundancy | 3.4 | |
CC(1/2) | 0.995 | 0.612 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.6 | 293 | 0.1 M Tris (base) bicine pH 8.2 - 8.8, 17 - 21% v/v PEG 500 MME, 8 - 10% w/v PEG 20000. Before setting up the drops 13 mg ml-1 Vc1313-LBD was mixed with 10 mM D-lysine from a 200 mM stock. The protein-ligand mixture was then mixed with reservoir solution in a 3:1 ratio. Before flash freezing the crystal in liquid nitrogen, the PEG concentrations were raised to 23% v/v PEG 500*MME, 12% w/v PEG 20000. |