6T2S
Prominent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293.15 | 1 M lithuim chloride, 1 M sodium citrate pH 4.0 and 20% PEG 6000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.24 | 70.97 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 156.62 | α = 90 |
b = 156.62 | β = 90 |
c = 197.051 | γ = 120 |
Symmetry | |
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Space Group | P 61 2 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 PILATUS3 6M | 2018-10-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9796 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 3.3 | 197.05 | 100 | 0.992 | 5.1 | 21.2 | 22156 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 3.3 | 3.56 | 0.679 | 1.7 |
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 | 3.3 | 135.637 | 22092 | 1097 | 99.937 | 0.202 | 0.1991 | 0.2533 | 61.144 |
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] | |
-0.885 | -0.443 | -0.885 | 2.871 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.03 |
r_dihedral_angle_4_deg | 22.423 |
r_dihedral_angle_3_deg | 21.347 |
r_dihedral_angle_1_deg | 11.151 |
r_lrange_it | 4.792 |
r_lrange_other | 4.792 |
r_mcangle_it | 2.794 |
r_mcangle_other | 2.794 |
r_scangle_other | 2.777 |
r_scangle_it | 2.775 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5811 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 111 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
GDA | data collection |
Aimless | data scaling |
PHASER | phasing |
Coot | model building |
DIALS | data reduction |