6RUU
Pseudokinase domain of human IRAK3
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2QKW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 293.15 | 20C, 8mg/mL protein, hanging drop vapour diffusion, 2uL :1uL drop ratio (protein:precipitant) + 1mL reservoir, streak seeding from 1:100 seed stock (original seed stock: 10 uL from drops containing previously obtained crystals +50 uL precipitant mix, crushed by vortexing with seed bead, diluted in precipitant mix), crystals appeared after 2-3 days, harvested after 5-7 days, overnight soaking with 1:1 v/v of 5 mM Ethylmercury Phosphate in stabilising solution, Cryo: Precipitant mix +30% Glycerol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.22 | 70.87 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.55 | α = 90 |
b = 167.16 | β = 90 |
c = 179.51 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 PILATUS3 6M | 2018-10-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 1.007 | Diamond | I24 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 49.056 | 92.2 | 0.28 | 0.285 | 0.052 | 0.998 | 12.1 | 29.4 | 28005 | 2 | 77.94 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.959 | 3.307 | 59.6 | 2.4 | 2.45 | 0.438 | 0.702 | 1.8 | 30.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2QKW | 2.95 | 48.65 | 1.34 | 21496 | 1119 | 61.65 | 0.2299 | 0.2283 | 0.26 | 90.74 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 6.9687 |
f_angle_d | 0.627 |
f_chiral_restr | 0.0436 |
f_plane_restr | 0.0035 |
f_bond_d | 0.0033 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6186 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 66 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
MxCuBE | data collection |
XDS | data reduction |
Aimless | data scaling |
STARANISO | data scaling |
MoRDa | phasing |
BALBES | phasing |
PARROT | phasing |
Coot | model building |