8ERX
Structure of chimeric HLA-A*11:01-A*02:01 bound to HIV-1 RT peptide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5HHN | 5HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB |
experimental model | PDB | 1S9W | 5HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB |
experimental model | PDB | 4QRT | 5HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB |
experimental model | PDB | 5VGE | 5HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB |
experimental model | PDB | 1Q94 | 5HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB |
experimental model | PDB | 2BNR | 5HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB |
experimental model | PDB | 6RPB | 5HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 294.15 | 0.02 Sodium/Potassium phosphate, 0.1 M BIS-TRIS propane pH 8.5, 18-22% PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.6 | 52.69 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.355 | α = 90 |
b = 79.324 | β = 116.1 |
c = 57.645 | 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 PILATUS3 6M | 2021-12-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.979 | APS | 19-ID |
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) | 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 | 15 | 99.6 | 0.119 | 0.141 | 0.075 | 8.7 | 3.6 | 30209 | 20.1 |
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 | 2.03 | 99.7 | 0.416 | 0.492 | 0.259 | 0.859 | 3.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 5HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB | 2.07 | 14.93 | 1.38 | 27641 | 1397 | 99.55 | 0.1941 | 0.1922 | 0.2311 | 24.2865 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3135 |
Nucleic Acid Atoms | |
Solvent Atoms | 359 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
PHASER | phasing |