4WDI
Weak TCR binding to an unstable insulin epitope drives type 1 diabetes
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 291 | 20% PEG 3350, 0.2 M Sodium malonate, and 0.1 M Bis-Tris Propane, pH 6.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.18 | 43.64 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.93 | α = 68.11 |
b = 62.69 | β = 85.79 |
c = 72.67 | γ = 85.18 |
Symmetry | |
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Space Group | P 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 PILATUS 2M | mirrors | 2012-02-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.917 | Diamond | I04-1 |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.313 | 29.518 | 90.2 | 0.068 | 0.12 | 0.081 | 8.6 | 2.1 | 30132 | 30132 |
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 | 2.31 | 2.37 | 91.5 | 0.351 | 0.351 | 0.43 | 2.2 | 2.2 | 2261 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.313 | 29.518 | 30131 | 1527 | 100 | 0.21 | 0.2061 | 0.2834 | RANDOM | 32.807 |
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] | |
1.01 | -0.54 | -0.1 | 0.25 | 1.46 | -2.24 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.718 |
r_dihedral_angle_4_deg | 19.993 |
r_dihedral_angle_3_deg | 18.666 |
r_dihedral_angle_1_deg | 7.39 |
r_scangle_it | 2.637 |
r_scbond_it | 1.75 |
r_angle_refined_deg | 1.598 |
r_mcangle_it | 1.086 |
r_angle_other_deg | 0.89 |
r_mcbond_it | 0.6 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6388 |
Nucleic Acid Atoms | |
Solvent Atoms | 160 |
Heterogen Atoms | 24 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
SCALA | data scaling |
PHASER | phasing |
GDA | data collection |
GDA | data reduction |