3MJ6
Crystal structure of the gammadelta T cell costimulatory receptor Junctional Adhesion Molecule-Like Protein, JAML
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.25 | 295 | 3.25 M NA-FORMATE, 0.1 M IMIDAZOLE, pH 7.25, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.58 | 52.36 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.946 | α = 90 |
b = 61.946 | β = 90 |
c = 82.477 | γ = 90 |
Symmetry | |
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Space Group | P 43 |
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 210 | KOHZU: DOUBLE CRYSTAL SI(111) | 2005-02-17 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.1 | 1.07812, 0.99984 | ALS | 8.2.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.19 | 50 | 99.7 | 0.083 | 0.083 | 11.1 | 3.6 | 15924 | 34.9 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.19 | 2.24 | 99.2 | 0.415 | 0.415 | 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 | MAD | THROUGHOUT | OBTAINED BY MAD PHASING OF A TA6BR12 SOAKED JAML CRYSTAL AND SUBSEQUENT MR INTO THE NATIVE HIGH RESOLUTION DATA | 2.19 | 50 | 15098 | 799 | 99.3 | 0.172 | 0.17 | 0.213 | RANDOM | 37.609 |
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] | |
0.16 | 0.16 | -0.33 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.55 |
r_dihedral_angle_4_deg | 22.573 |
r_dihedral_angle_3_deg | 16.657 |
r_dihedral_angle_1_deg | 8.007 |
r_scangle_it | 4.414 |
r_scbond_it | 2.625 |
r_angle_refined_deg | 1.716 |
r_mcangle_it | 1.642 |
r_angle_other_deg | 1.296 |
r_mcbond_it | 0.862 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1828 |
Nucleic Acid Atoms | |
Solvent Atoms | 129 |
Heterogen Atoms | 77 |
Software
Software | |
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Software Name | Purpose |
SHELX | model building |
RESOLVE | model building |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
SHELX | phasing |
RESOLVE | phasing |