7C2W

Crystal Structure of IRAK4 kinase in complex with a small molecule inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NRU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	298	0.1 M sodium acetate pH 5.4, 2.3 M sodium malonate

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.63	α = 90
b = 140.802	β = 127.64
c = 86.496	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU		2010-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-002+	1.5

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	3.14	100	89.9	0.095	0.76	2.4	2.4		21131

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.14	3.21	86.8		0.38	0.75	2.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	2NRU	3.2	29.62	18229	977	89.22	0.2662	0.2614	0.355	RANDOM	34.886

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]
-0.2		-0.16	0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.013
r_dihedral_angle_4_deg	17.424
r_dihedral_angle_3_deg	16.452
r_dihedral_angle_1_deg	5.947
r_angle_refined_deg	1.134
r_angle_other_deg	0.718
r_symmetry_hbond_refined	0.393
r_nbd_refined	0.213
r_symmetry_vdw_other	0.197
r_xyhbond_nbd_refined	0.189
r_nbd_other	0.17
r_symmetry_vdw_refined	0.166
r_nbtor_other	0.081
r_xyhbond_nbd_other	0.074
r_chiral_restr	0.055
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9323
Nucleic Acid Atoms
Solvent Atoms	164
Heterogen Atoms	120

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing