5Y3M
Crystal structure of bovine TLR9 in complex with two DNAs (CpG DNA and TCGTTT DNA)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3WPE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 10%(w/v) PEG 4000 0.5M NaCl 0.1M Mes-NaOH pH 6.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.43 | 54.07 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 88.177 | α = 90 |
b = 68.693 | β = 100.64 |
c = 153.535 | γ = 90 |
Symmetry | |
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Space Group | P 1 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 | PIXEL | DECTRIS PILATUS 2M | 2015-06-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NE3A | 1.0000 | Photon Factory | AR-NE3A |
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 | 2.5 | 48.96 | 99.9 | 8 | 5.1 | 62911 |
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 | 3WPE | 2.5 | 48.96 | 59852 | 3058 | 99.9 | 0.22606 | 0.22512 | 0.24427 | RANDOM | 32.77 |
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] | |
0.46 | 0.55 | -1.58 | 0.86 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.106 |
r_dihedral_angle_4_deg | 14.284 |
r_dihedral_angle_3_deg | 13.282 |
r_dihedral_angle_1_deg | 6.063 |
r_long_range_B_refined | 2.289 |
r_long_range_B_other | 2.271 |
r_angle_refined_deg | 1.269 |
r_mcangle_it | 1.146 |
r_mcangle_other | 1.146 |
r_angle_other_deg | 1.01 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11574 |
Nucleic Acid Atoms | 426 |
Solvent Atoms | 134 |
Heterogen Atoms | 140 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
MOLREP | phasing |