8V2F | pdb_00008v2f

Crystal structure of IRAK4 kinase domain with compound 9

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291	1.8M ammonium citrate, 1.75mM compound (1.8% DMSO)

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 142.87	α = 90
b = 140.68	β = 124
c = 89.02	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	PIXEL	DECTRIS PILATUS 6M		2021-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.97915	SSRF	BL18U1

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	2.09	49.14	99.86	0.1389	0.1507	0.0578	0.997	13.07	6.8		85963			35.99

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)	Redundancy	Number Unique Reflections (All)
1	2.09	2.165	99.95		1.17	1.265	0.477	0.668	2.35	7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.09	49.14	81617	4334	99.9	0.17014	0.16814	0.18	0.20754	0.21	RANDOM	43.936

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]
0.94		0.83	-3.12		0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.431
r_dihedral_angle_4_deg	23.428
r_dihedral_angle_3_deg	16.026
r_long_range_B_other	10.819
r_long_range_B_refined	10.808
r_scangle_other	8.267
r_dihedral_angle_1_deg	6.304
r_mcangle_it	6.117
r_mcangle_other	6.116
r_scbond_it	5.43
r_scbond_other	5.43
r_mcbond_it	4.146
r_mcbond_other	4.146
r_angle_refined_deg	1.589
r_angle_other_deg	1.34
r_chiral_restr	0.074
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	9397
Nucleic Acid Atoms
Solvent Atoms	619
Heterogen Atoms	175

Software

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