8V2L

Crystal structure of IRAK4 kinase domain with compound 8

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		in house structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.7	293	0.1M MES, pH6.7, 0.2M Ammonium sulfate, 25% w/v PEG5000 MME

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.735	α = 90
b = 113.477	β = 90
c = 134.828	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 EIGER X 16M		2021-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.978565	SSRF	BL10U2

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	2.43	71.85	99.65	0.1685	0.1886	0.08328	0.992	7.88	4.9		49657			40

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	2.43	2.517	99.94		0.895	0.998	0.4349	0.84	2.14	5.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.43	71.85	47140	2490	99.79	0.25522	0.25273	0.30246	RANDOM	48.604

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]
2.13			2.22		-4.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.028
r_dihedral_angle_4_deg	24.061
r_dihedral_angle_3_deg	16.42
r_long_range_B_refined	8.31
r_long_range_B_other	8.309
r_dihedral_angle_1_deg	6.835
r_mcangle_it	5.147
r_mcangle_other	5.147
r_scangle_other	4.689
r_mcbond_it	3.045
r_mcbond_other	3.045
r_scbond_it	2.794
r_scbond_other	2.794
r_angle_refined_deg	1.368
r_angle_other_deg	1.219
r_chiral_restr	0.05
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002
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 Atoms	Number
Protein Atoms	9151
Nucleic Acid Atoms
Solvent Atoms	338
Heterogen Atoms	144

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing