8V2L

Crystal structure of IRAK4 kinase domain with compound 8


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherin house structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.72930.1M MES, pH6.7, 0.2M Ammonium sulfate, 25% w/v PEG5000 MME
Crystal Properties
Matthews coefficientSolvent content
2.4750.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.735α = 90
b = 113.477β = 90
c = 134.828γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL10U20.978565SSRFBL10U2

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.4371.8599.650.16850.18860.083280.9927.884.94965740
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)RedundancyNumber Unique Reflections (All)
12.432.51799.940.8950.9980.43490.842.145.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.4371.8547140249099.790.255220.252730.30246RANDOM48.604
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]
2.132.22-4.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.028
r_dihedral_angle_4_deg24.061
r_dihedral_angle_3_deg16.42
r_long_range_B_refined8.31
r_long_range_B_other8.309
r_dihedral_angle_1_deg6.835
r_mcangle_it5.147
r_mcangle_other5.147
r_scangle_other4.689
r_mcbond_it3.045
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.028
r_dihedral_angle_4_deg24.061
r_dihedral_angle_3_deg16.42
r_long_range_B_refined8.31
r_long_range_B_other8.309
r_dihedral_angle_1_deg6.835
r_mcangle_it5.147
r_mcangle_other5.147
r_scangle_other4.689
r_mcbond_it3.045
r_mcbond_other3.045
r_scbond_it2.794
r_scbond_other2.794
r_angle_refined_deg1.368
r_angle_other_deg1.219
r_chiral_restr0.05
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9151
Nucleic Acid Atoms
Solvent Atoms338
Heterogen Atoms144

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing