7PDX
Crystal structure of parent MAGE-A10 TCR (728)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293.15 | 0.1M PCTP pH 7.0, 25% w/v PEG 1500 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.486 | 50.56 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 54.93 | α = 101.94 |
b = 59.171 | β = 105.87 |
c = 86.02 | γ = 104.69 |
Symmetry | |
---|---|
Space Group | P 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 PILATUS3 6M | 2018-05-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.97625 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.27 | 79.011 | 86.2 | 0.117 | 0.166 | 0.117 | 0.957 | 4.3 | 1.5 | 38348 | 14.61 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.27 | 2.34 | 85 | 0.21 | 0.297 | 0.21 | 0.898 | 2.3 | 1.5 |
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 (All) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 7PDW | 2.27 | 79.01 | 38335 | 1873 | 86.177 | 0.195 | 0.192 | 0.2516 | Random | 32.761 |
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] | |
0.721 | 1.047 | -0.062 | 2.877 | -0.526 | -2.822 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.762 |
r_dihedral_angle_4_deg | 15.91 |
r_dihedral_angle_3_deg | 15.399 |
r_dihedral_angle_1_deg | 8.234 |
r_lrange_it | 7.158 |
r_lrange_other | 7.142 |
r_scangle_other | 5.112 |
r_scangle_it | 5.111 |
r_mcangle_it | 4.336 |
r_mcangle_other | 4.336 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 6744 |
Nucleic Acid Atoms | |
Solvent Atoms | 299 |
Heterogen Atoms | 7 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
MOSFLM | data reduction |
Coot | model building |
PHASER | phasing |