2P5E
Crystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC Reveal Native Diagonal Binding Geometry
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2F53 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 293 | 85 mM HEPES, 8.5% Isopropanol, 17% PEG 4000, 15% Glycerol, pH 7.5, VAPOR DIFFUSION, temperature 293K, pH 7.50 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 48.67 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.002 | α = 90 |
b = 51.771 | β = 98.24 |
c = 118.27 | 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 | CCD | ADSC QUANTUM 4 | MIRROR + MONOCHROMATOR | 2005-07-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX14.1 | SRS | PX14.1 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.887 | 117 | 69966 |
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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2F53 | 1.89 | 117.04 | 66411 | 3552 | 97.44 | 0.18071 | 0.17777 | 0.23579 | RANDOM | 12.457 |
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] | |
1.29 | 1.52 | 0.3 | -1.16 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 24.273 |
r_dihedral_angle_4_deg | 10.558 |
r_dihedral_angle_3_deg | 8.812 |
r_scangle_it | 7.091 |
r_scbond_it | 5.409 |
r_mcangle_it | 3.544 |
r_mcbond_it | 3.072 |
r_dihedral_angle_1_deg | 2.817 |
r_angle_refined_deg | 1.173 |
r_mcbond_other | 0.86 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6568 |
Nucleic Acid Atoms | |
Solvent Atoms | 739 |
Heterogen Atoms | 93 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |