8V1O

Crystal structure of IRAK4 kinase domain with compound 4


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.92910.2M Ammonium sulfate, 0.1M MES, pH6.9, 30% w/v PEG5000 MME
Crystal Properties
Matthews coefficientSolvent content
2.4750.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.85α = 90
b = 140.49β = 123.73
c = 87.94γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2018-08-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.97633APS21-ID-D

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
12.9247.8798.90.20.2160.0820.9927.7730999
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)
12.923.0899.90.8680.9350.3460.8527.2

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 REPLACEMENTTHROUGHOUT2.9247.8729473152498.830.218860.216430.2655RANDOM60.861
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]
3.292.04-3.81-1.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.498
r_dihedral_angle_4_deg22.938
r_dihedral_angle_3_deg16.209
r_long_range_B_refined10.985
r_long_range_B_other10.985
r_scangle_other7.93
r_mcangle_it7.719
r_mcangle_other7.718
r_dihedral_angle_1_deg7.06
r_scbond_it5.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.498
r_dihedral_angle_4_deg22.938
r_dihedral_angle_3_deg16.209
r_long_range_B_refined10.985
r_long_range_B_other10.985
r_scangle_other7.93
r_mcangle_it7.719
r_mcangle_other7.718
r_dihedral_angle_1_deg7.06
r_scbond_it5.01
r_scbond_other5.01
r_mcbond_it5.006
r_mcbond_other5.002
r_angle_refined_deg1.511
r_angle_other_deg1.188
r_chiral_restr0.059
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms9160
Nucleic Acid Atoms
Solvent Atoms118
Heterogen Atoms146

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
REFMACphasing
XDSdata reduction