4E41
Structural basis for the recognition of mutant self by a tumor-specific, MHC class II-restricted T cell receptor G4
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION | 8 | 298 | 20% (wt/vol) polyethylene glycol 1000, 0.2 M calcium acetate, 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, temperature 298K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.43 | 49.33 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 126.133 | α = 90 |
| b = 175.611 | β = 110.75 |
| c = 88.646 | γ = 90 |
| Symmetry | |
|---|---|
| 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 | CCD | ADSC QUANTUM 315 | 2007-04-19 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | NSLS BEAMLINE X29A | 1.0 | NSLS | X29A |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.6 | 30 | 97.2 | 53716 | 2 | 2 | |||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 2.6 | 2.7 | 83.8 | 0.269 | 2.6 | 3.1 | |||||||||||||
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 | PDB entry 2IAM | 2.6 | 30 | 51068 | 2704 | 97.23 | 0.20076 | 0.19743 | 0.26374 | RANDOM | 49.044 | ||||||
| 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] | |
| -1.52 | -1.31 | -0.69 | 1.27 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.804 |
| r_dihedral_angle_3_deg | 19.04 |
| r_dihedral_angle_4_deg | 18.972 |
| r_dihedral_angle_1_deg | 10.922 |
| r_scangle_it | 2.537 |
| r_angle_refined_deg | 1.687 |
| r_scbond_it | 1.491 |
| r_mcangle_it | 1.227 |
| r_mcbond_it | 0.641 |
| r_nbtor_refined | 0.31 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 12805 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 172 |
| Heterogen Atoms | 2 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| ADSC | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
