2CDG
Structure and binding kinetics of three different human CD1d-alpha- Galactosylceramide-specific T cell receptors (TCR 5B)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2CDF | PDB ENTRY 2CDF |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 200 MM DI-AMMONIUM TARTRATE, 20 % PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.062 | α = 90 |
b = 64.062 | β = 90 |
c = 185 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 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 CCD | 2003-11-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX14.2 | SRS | PX14.2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 18 | 96.6 | 0.12 | 10.4 | 5.4 | 13750 | 0.5 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.67 | 87.4 | 0.55 | 2.2 |
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 | PDB ENTRY 2CDF | 2.6 | 61.66 | 13033 | 656 | 96 | 0.222 | 0.217 | 0.318 | RANDOM | 22.94 |
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] | |
-0.04 | -0.02 | -0.04 | 0.06 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.922 |
r_dihedral_angle_3_deg | 19.471 |
r_dihedral_angle_4_deg | 14.208 |
r_dihedral_angle_1_deg | 6.489 |
r_mcangle_it | 3.701 |
r_scangle_it | 3.515 |
r_scbond_it | 2.631 |
r_mcbond_it | 2.495 |
r_angle_refined_deg | 1.298 |
r_nbtor_refined | 0.301 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3392 |
Nucleic Acid Atoms | |
Solvent Atoms | 61 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |