8F0L
Crystal Structure of the Human T cell Receptor CD3(EPSILON) N-Terminal Peptide Complexed with ADI-26906 FAB
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | Crystals of the ADI-26906 Fab complexed to CD3 epsilon N13 peptide were obtained by the sitting drop vapor diffusion method. The ADI-26906 Fab buffered in PBS, was first buffer-exchanged into 20 mM Bis-Tris pH 6.0 and 150 mM NaCl. The Fab (0.31 mM) was mixed with the N13 peptide (7.8 mM) at a Fab:peptide ratio of 1:25 and incubated on ice for 1.5 h. A BCS screen (Molecular Dimensions Ltd.) was set up using a mosquito crystallization robot (STP Labtech), with each drop consisting of 100 nL protein and 100 nL of reservoir solution, and left to equilibrate against a 40 uL reservoir solution at 293 K. After a few days, crystals were obtained in condition A6 (0.1 M MES pH 6.5, 25% w/v PEG Smear Broad). |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.21 | 44.46 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.634 | α = 90 |
b = 53.084 | β = 99.82 |
c = 113.934 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 2021-04-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX IV BEAMLINE BioMAX | 0.9763 | MAX IV | BioMAX |
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 | 1.81 | 66.31 | 99.9 | 0.074 | 0.08 | 0.03 | 0.998 | 13.8 | 6.9 | 79385 |
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 | 1.81 | 1.841 | 99.6 | 0.872 | 0.942 | 0.352 | 0.746 | 2.1 | 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-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4IRZ | 1.81 | 48.6 | 79377 | 99.9 | 0.166 | 0.195 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6703 |
Nucleic Acid Atoms | |
Solvent Atoms | 712 |
Heterogen Atoms | 42 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |