4R09
Crystal structure of human TLR8 in complex with ORN06S
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5 | 293 | 12-14% (w/v) PEG 3350, 0.2-0.3M potassium formate, 0.1M sodium citrate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.81 | 56.15 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 86.683 | α = 90 |
b = 141.342 | β = 89.46 |
c = 170.042 | 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 | 95 | CCD | ADSC QUANTUM 315r | 2013-04-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 1.0000 | Photon Factory | BL-5A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.6 | 50 | 99.8 | 0.148 | 22.2 | 3.8 | 114230 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2.62 | 31.56 | 115689 | 6113 | 98.9 | 0.21967 | 0.21614 | 0.28508 | RANDOM | 63.343 |
Temperature Factor Modeling | ||||||
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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 | -0.01 | -0.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.435 |
r_dihedral_angle_3_deg | 18.283 |
r_dihedral_angle_4_deg | 17.512 |
r_long_range_B_refined | 8.7 |
r_long_range_B_other | 8.7 |
r_dihedral_angle_1_deg | 7.648 |
r_mcangle_it | 6.283 |
r_mcangle_other | 6.283 |
r_scangle_other | 5.998 |
r_mcbond_it | 4.102 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 24106 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 789 |
Software
Software | |
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Software Name | Purpose |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |