6CW9
Structure of alpha-GC[8,16P] bound by CD1d and in complex with the Va14Vb8.2 TCR
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2Q7Y |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.1 | 295 | 0.06M Citric acid, 0.04M BIS-TRIS propane, 16% PEG 3350, pH 4.1 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.04 | 59.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.223 | α = 90 |
b = 192.026 | β = 90 |
c = 151.113 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 PILATUS 6M | 2017-10-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.979 | SSRL | BL9-2 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 50.01 | 99.5 | 0.085 | 0.091 | 0.033 | 7.4 | 7.3 | 77934 |
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 | 99.5 | 0.566 | 0.613 | 0.231 | 0.874 | 6.8 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2Q7Y | 2 | 40.5 | 73728 | 3899 | 99.52 | 0.1914 | 0.1898 | 0.2208 | RANDOM | 38.525 |
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] | |
0.02 | -0.02 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.715 |
r_dihedral_angle_4_deg | 18.465 |
r_dihedral_angle_3_deg | 12.689 |
r_dihedral_angle_1_deg | 6.222 |
r_angle_refined_deg | 1.357 |
r_angle_other_deg | 0.868 |
r_chiral_restr | 0.079 |
r_bond_refined_d | 0.009 |
r_gen_planes_refined | 0.005 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 6370 |
Nucleic Acid Atoms | |
Solvent Atoms | 441 |
Heterogen Atoms | 144 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALEPACK | data scaling |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
PHASER | phasing |