8BXY
FimH in complex with alpha1,6 core-fucosylated oligomannose-3, crystallized in the trigonal space group
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2VCO |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 9 | 291 | 1.1 M Lithium sulphate; 0.1 M Tris-HCl pH 9.0; 10 mM nickel chloride |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.65 | 53.66 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 91.056 | α = 90 |
b = 91.056 | β = 90 |
c = 79.578 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 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 | DECTRIS EIGER X 16M | 2018-11-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 2 | 0.987 | SOLEIL | PROXIMA 2 |
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 | 1.45 | 56.076 | 95.16 | 0.075 | 0.077 | 0.017 | 0.9996 | 19.325 | 20.11 | 56199 | 24.99 |
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 | 1.45 | 1.556 | 21.9 | 1.837 | 1.949 | 0.639 | 0.615 | 1.6 | 16.95 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.45 | 56.076 | 56198 | 1481 | 82.867 | 0.155 | 0.1532 | 0.2054 | 32.691 |
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] | |
0.603 | 0.301 | 0.603 | -1.955 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_rigid_bond_restr | 23.863 |
r_dihedral_angle_6_deg | 17.432 |
r_scbond_it | 16.344 |
r_scangle_it | 13.632 |
r_dihedral_angle_3_deg | 11.962 |
r_lrange_it | 10.166 |
r_dihedral_angle_1_deg | 8.084 |
r_dihedral_angle_2_deg | 5.984 |
r_mcangle_it | 5.584 |
r_mcbond_it | 5.091 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2392 |
Nucleic Acid Atoms | |
Solvent Atoms | 345 |
Heterogen Atoms | 151 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
PHENIX | model building |
autoPROC | data processing |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |