8QJD
T6SS-linked Rhs repeat protein - Salmonella bongori Rhs-core domain
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 292.15 | Protein was diluted to 3 mg/ml using MonoQ buffer A and 1 ul was mixed with 2 ul of reservoir solution (0.1 M MES pH 7, 20% PEE 270, 3.67% acetone) in a hanging drop vapor diffusion experiment at 19 deg C to obtain the crystals for the native dataset used for SIRAS phasing and for refinement. Before the diffraction experiment, crystals were cryoprotected by soaking in a solution consisting of 0.1M MES pH7 and 35% PEE270. For the Hg(II) derivative dataset used in SIRAS phasing, the crystal was grown in a similar fashion but using a reservoir solution comprising 0.1 M HEPES pH 7, 20% PEE 270. Derivatisation was performed by soaking the crystal for a couple of minutes in reservoir solution supplemented with 12.5 mM thimerosal. Crystals were back soaked and cryoprotected in mother liquor with an increased PEE 270 concentration (35%). |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 42.72 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 99.071 | α = 90 |
b = 118.26 | β = 105.52 |
c = 131.757 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | PSI PILATUS 6M | 2014-05-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1 | SLS | X06SA |
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 | 2.203 | 49.17 | 99.61 | 0.08007 | 0.08671 | 0.03298 | 0.999 | 17.62 | 6.84 | 147230 | 37.86 |
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) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.203 | 2.281 | 97.11 | 0.8547 | 0.9292 | 0.836 | 2.32 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | SIRAS | FREE R-VALUE | 2.203 | 49.17 | 1.91 | 147188 | 14502 | 99.31 | 0.1837 | 0.1822 | 0.211 | 47.95 |
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 | 12.8221 |
f_angle_d | 0.6656 |
f_chiral_restr | 0.0461 |
f_plane_restr | 0.0055 |
f_bond_d | 0.0036 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 16859 |
Nucleic Acid Atoms | |
Solvent Atoms | 1209 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PHENIX | refinement |
Coot | model building |
ARP/wARP | model building |
BUCCANEER | phasing |
SHARP | phasing |
XDS | data scaling |
XDS | data reduction |