4TW1
Crystal structure of the octameric pore complex of the Staphylococcus aureus Bi-component Toxin LukGH
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | Drops consisted of 100 nl protein in 20 mM HEPES buffer pH 7.5 and 100 nl reservoir 30 mM MgCl2, 30 mM CaCl2, 0.1 M Na HEPES/MOPS buffer pH 7.5, 12.5 % v/v MPD, 12.5 % w/v PEG 1000, 12.5 % w/v PEG 3350. Crystals appeared after 7 days. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
4.39 | 71.96 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 135.497 | α = 90 |
b = 198.558 | β = 103.26 |
c = 179.535 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 225 mm CCD | 2013-12-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX II BEAMLINE I911-3 | 1.0000 | MAX II | I911-3 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.8 | 48.188 | 97.9 | 0.16 | 0.194 | 0.109 | 10.1 | 3.1 | 222018 | 222018 | 56.4 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.8 | 2.95 | 95.4 | 0.871 | 0.871 | 0.591 | 0.9 | 3.1 | 31557 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | THROUGHOUT | 3B07 prepared using CHAINSAW | 2.8 | 48 | 218497 | 2207 | 96 | 0.2387 | 0.2381 | 0.2923 | RANDOM | 36.001 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
4.69 | -3.36 | -1.99 | -1.01 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.491 |
r_dihedral_angle_3_deg | 20.748 |
r_dihedral_angle_4_deg | 20.721 |
r_dihedral_angle_1_deg | 8.109 |
r_mcangle_it | 3.887 |
r_scbond_it | 2.696 |
r_mcbond_it | 2.318 |
r_angle_refined_deg | 1.796 |
r_chiral_restr | 0.112 |
r_bond_refined_d | 0.013 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 37415 |
Nucleic Acid Atoms | |
Solvent Atoms | 205 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
XDS | data reduction |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
PHASER | phasing |
REFMAC | refinement |
XSCALE | data reduction |