7O23
C-terminal head domain of the trimeric autotransporter adhesin BpaC from Burkholderia pseudomallei fused to a GCN4 anchor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3S6L |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | Protein solution at 130 mg/mL in 20 mM Tris-HCl pH 8, 150 mM NaCl. Hit in JCSG IV, E10: 100 nL protein solution + 100 nL reservoir solution 0.1 M HEPES pH 6.5, 0.8 M (NH4)2SO4 Cryoprotection: add 400 nL of 0.15 M HEPES pH 6.5, 1.2 M (NH4)2SO4, 35% Glycerol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.61 | 53 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.39 | α = 90 |
b = 57.39 | β = 90 |
c = 516.53 | γ = 120 |
Symmetry | |
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Space Group | H 3 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 EIGER X 16M | 2019-10-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.97949 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.4 | 44.79 | 99.53 | 0.168 | 0.995 | 6.87 | 8 | 65740 | 6 | 12.07 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.4 | 1.45 | 99.28 | 1.061 | 0.657 | 1.39 | 7.5 |
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-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 3S6L | 1.4 | 44.79 | 1.71 | 65740 | 3239 | 99.48 | 0.184 | 0.2171 | 24 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 5.6287 |
f_angle_d | 0.8165 |
f_chiral_restr | 0.079 |
f_bond_d | 0.0061 |
f_plane_restr | 0.0043 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2031 |
Nucleic Acid Atoms | |
Solvent Atoms | 278 |
Heterogen Atoms | 13 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
pointless | data scaling |
Aimless | data scaling |
PHASER | phasing |
BUCCANEER | model building |
Coot | model building |