6RHW
Crystal structure of human CD11b I-domain (CD11b-I) in complex with Staphylococcus aureus octameric bi-component leukocidin LukGH
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1IDO | 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) |
Crystallization
Crystalization Experiments | ||||
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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. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.61 | 52.81 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 122.107 | α = 90 |
b = 122.107 | β = 90 |
c = 133.697 | γ = 90 |
Symmetry | |
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Space Group | P 4 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2018-11-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 1.072270 | ESRF | ID29 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||
1 | 2.748 | 45.081 | 53.8 | 0.31 | 0.347 | 0.09 | 0.996 | 7.8 | 12.6 | 14539 | 53.18 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.748 | 2.994 | 15 | 1.668 | 1.739 | 0.486 | 0.627 | 1.8 | 12.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 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) | 2.75 | 45.08 | 1.33 | 14518 | 658 | 53.66 | 0.2412 | 0.2393 | 0.2812 | Random selection | 61.12 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.4293 |
f_angle_d | 0.7813 |
f_chiral_restr | 0.0478 |
f_plane_restr | 0.0043 |
f_bond_d | 0.0031 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5730 |
Nucleic Acid Atoms | |
Solvent Atoms | 2 |
Heterogen Atoms | 25 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
STARANISO | data scaling |
Aimless | data scaling |
PHASER | phasing |
Coot | model building |