7ZT4
Structure of E8 TCR in complex with human MR1 bound to 6FP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5U6Q |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.2 M Sodium iodide, 0.1 M Bis-Tris propane pH 8.5 and 20 % w/v PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.12 | 60.53 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 91.71 | ¦Á = 90 |
b = 104.39 | ¦Â = 90 |
c = 117.97 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 EIGER2 XE 16M | 2020-07-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9763 | Diamond | I03 |
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 | 2.02 | 58.99 | 100 | 0.14 | 0.145 | 0.037 | 0.999 | 13.1 | 15.2 | 74899 |
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 | 2.02 | 2.05 | 100 | 4.786 | 4.946 | 1.234 | 0.299 | 0.6 | 15.7 |
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 | 5U6Q | 2.02 | 58.99 | 71062 | 3762 | 99.97 | 0.236 | 0.23431 | 0.26764 | RANDOM | 53.513 |
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] | |
-0.81 | -1.78 | 2.59 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.038 |
r_dihedral_angle_3_deg | 16.084 |
r_dihedral_angle_4_deg | 15.476 |
r_dihedral_angle_1_deg | 7.67 |
r_long_range_B_refined | 5.447 |
r_long_range_B_other | 5.435 |
r_mcangle_it | 1.622 |
r_mcangle_other | 1.621 |
r_angle_refined_deg | 1.476 |
r_scangle_other | 1.418 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6369 |
Nucleic Acid Atoms | |
Solvent Atoms | 234 |
Heterogen Atoms | 13 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
xia2 | data scaling |
PHASER | phasing |