5C0B
1E6 TCR in complex with HLA-A02 carrying RQFGPDFPTI
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 291 | 0.1M HEPES, pH 7.5, 15% PEG 4000, 0.2M sodium acetate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.75 | 55.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 43.94 | α = 96.98 |
b = 100.28 | β = 98.05 |
c = 122.44 | γ = 96.53 |
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 6M | 2012-03-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.97630 | Diamond | I03 |
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 | 2.03 | 42.76 | 97.6 | 0.05 | 0.069 | 0.046 | 8 | 2 | 128366 | 128366 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.03 | 2.08 | 96.7 | 0.268 | 0.268 | 0.428 | 2.8 | 1.9 | 9447 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | PDB entry 3UTQ for the MHC part and 4UTQ for the TCR part. | 2.03 | 42.76 | 121919 | 6446 | 97.55 | 0.194 | 0.1921 | 0.2307 | RANDOM | 52.559 |
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] | |
1.91 | 0.29 | -0.77 | 0.95 | 0.6 | -2.68 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.023 |
r_dihedral_angle_4_deg | 20.99 |
r_dihedral_angle_3_deg | 19.315 |
r_dihedral_angle_1_deg | 7.527 |
r_mcangle_it | 2.306 |
r_angle_refined_deg | 1.923 |
r_mcbond_other | 1.504 |
r_mcbond_it | 1.503 |
r_angle_other_deg | 1.269 |
r_chiral_restr | 0.144 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13402 |
Nucleic Acid Atoms | |
Solvent Atoms | 472 |
Heterogen Atoms | 306 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |