6RPA
Crystal structure of the T-cell receptor NYE_S2 bound to HLA A2*01-SLLMWITQV
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 5E00 | 5e00 (chains A and B), 3REV (chain A) and 4DZB (chain B) |
experimental model | PDB | 3REV | 5e00 (chains A and B), 3REV (chain A) and 4DZB (chain B) |
experimental model | PDB | 4DZB | 5e00 (chains A and B), 3REV (chain A) and 4DZB (chain B) |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.02 M sodium/potassium phosphate, 20 % PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.26 | 62.25 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 173.16 | α = 90 |
b = 84.25 | β = 129.81 |
c = 111.51 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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-F | 2017-09-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.91587 | Diamond | I04-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.56 | 66.51 | 99.3 | 0.064 | 0.025 | 0.999 | 17.9 | 7.66 | 37679 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.56 | 2.6 | 99.7 | 2.07 | 0.775 | 0.637 | 0.96 | 7.94 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 5e00 (chains A and B), 3REV (chain A) and 4DZB (chain B) | 2.56 | 66.51 | 37679 | 1945 | 99.31 | 0.25209 | 0.2499 | 0.29324 | RANDOM | 80.735 |
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] | |
3.15 | -3.46 | 3.12 | -0.21 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.197 |
r_dihedral_angle_3_deg | 14.575 |
r_dihedral_angle_4_deg | 13.361 |
r_long_range_B_refined | 9.727 |
r_long_range_B_other | 9.727 |
r_dihedral_angle_1_deg | 6.076 |
r_mcangle_it | 5.427 |
r_mcangle_other | 5.427 |
r_scangle_other | 4.541 |
r_mcbond_it | 3.256 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 6277 |
Nucleic Acid Atoms | |
Solvent Atoms | 49 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
xia2 | data scaling |
PHASER | phasing |