6RHW
Crystal structure of human CD11b I-domain (CD11b-I) in complex with Staphylococcus aureus octameric bi-component leukocidin LukGH
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ESRF BEAMLINE ID29 |
Synchrotron site | ESRF |
Beamline | ID29 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-11-22 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 1.072270 |
Spacegroup name | P 4 21 2 |
Unit cell lengths | 122.107, 122.107, 133.697 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 45.080 - 2.750 |
R-factor | 0.2412 |
Rwork | 0.239 |
R-free | 0.28120 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | LukGH dimer from the structure of its complex with mouse CD11b I-domain (CD11b-I) and the modified huCD11b-I domain (PDB code 1IDO) lacking the C-terminal alpha-helix (residues 303-315) |
RMSD bond length | 0.003 |
RMSD bond angle | 0.781 |
Data reduction software | XDS (January 26, 2018) |
Data scaling software | STARANISO (2.2.7 (8-Dec-2018)) |
Phasing software | PHASER (2.7.17) |
Refinement software | PHENIX (1.14rc1_3177) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 45.081 | 2.994 |
High resolution limit [Å] | 2.748 | 2.748 |
Rmerge | 0.310 | 1.668 |
Rmeas | 0.347 | 1.739 |
Rpim | 0.090 | 0.486 |
Number of reflections | 14539 | 902 |
<I/σ(I)> | 7.8 | 1.8 |
Completeness [%] | 53.8 | 15 |
Redundancy | 12.6 | 12.5 |
CC(1/2) | 0.996 | 0.627 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 295 | Crystallization drops were prepared by mixing 1.0 uL LukGH/huCD11b-I complex (5.2 mg/mL) in 25 mM HEPES (pH 7.5), 1 mM MgCl2 with 0.5 uL reservoir solution containing 30% (v/v) Jeffamine-600 and 10% (v/v) DMSO. |