8V2F

Crystal structure of IRAK4 kinase domain with compound 9


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherinternal structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72911.8M ammonium citrate, 1.75mM compound (1.8% DMSO)
Crystal Properties
Matthews coefficientSolvent content
2.4950.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.87α = 90
b = 140.68β = 124
c = 89.02γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U10.97915SSRFBL18U1

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
12.0949.1499.860.13890.15070.05780.99713.076.88596335.99
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)
12.092.16599.951.171.2650.4770.6682.357

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 REPLACEMENTTHROUGHOUT2.0949.1481617433499.90.170140.168140.20754RANDOM43.936
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]
0.940.83-3.120.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.431
r_dihedral_angle_4_deg23.428
r_dihedral_angle_3_deg16.026
r_long_range_B_other10.819
r_long_range_B_refined10.808
r_scangle_other8.267
r_dihedral_angle_1_deg6.304
r_mcangle_it6.117
r_mcangle_other6.116
r_scbond_it5.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.431
r_dihedral_angle_4_deg23.428
r_dihedral_angle_3_deg16.026
r_long_range_B_other10.819
r_long_range_B_refined10.808
r_scangle_other8.267
r_dihedral_angle_1_deg6.304
r_mcangle_it6.117
r_mcangle_other6.116
r_scbond_it5.43
r_scbond_other5.43
r_mcbond_it4.146
r_mcbond_other4.146
r_angle_refined_deg1.589
r_angle_other_deg1.34
r_chiral_restr0.074
r_bond_refined_d0.01
r_gen_planes_refined0.008
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 Atoms9397
Nucleic Acid Atoms
Solvent Atoms619
Heterogen Atoms175

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing