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Pseudokinase domain of human IRAK3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QKW
Crystallization Crystalization Experiments 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 Matthews coefficient Solvent content 4.22 70.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.55 α = 90 b = 167.16 β = 90 c = 179.51 γ = 90
Symmetry Space Group P 21 21 2
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 PILATUS3 6M 2018-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 1.007 Diamond I24
Data Collection Overall 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 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 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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2QKW 2.95 48.65 1.34 21496 1119 61.65 0.2299 0.2283 0.2291 0.26 0.2536 90.74
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]
RMS Deviations 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 Non-Hydrogen Atoms Number Protein Atoms 6186 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 66
Software Software 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