8WTF | pdb_00008wtf

The Crystal Structure of IRAK4 from Biortus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6EGF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M Ammonium sulfate,0.1M BisTris,5.5,25% w/vPEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.449	α = 90
b = 93.061	β = 99.146
c = 60.925	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		2021-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1	SPring-8	BL45XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	46.53	99.7	0.147	6.8	4.1		19106

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05			0.515

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2	46.53	19102	973	99.635	0.183	0.18	0.19	0.2363	0.25	31.171

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]
-1.004		-1.101	2.932		-1.497

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.825
r_dihedral_angle_4_deg	22.93
r_lrange_other	14.517
r_lrange_it	14.483
r_scangle_it	13.021
r_scangle_other	13.011
r_dihedral_angle_3_deg	11.573
r_scbond_it	10.545
r_scbond_other	10.528
r_mcangle_it	8.42
r_mcangle_other	8.418
r_mcbond_it	7.358
r_mcbond_other	7.357
r_dihedral_angle_1_deg	5.415
r_angle_refined_deg	1.151
r_angle_other_deg	1.075
r_nbd_refined	0.154
r_symmetry_nbd_other	0.153
r_nbtor_refined	0.144
r_nbd_other	0.113
r_symmetry_nbd_refined	0.11
r_xyhbond_nbd_refined	0.099
r_symmetry_xyhbond_nbd_refined	0.086
r_symmetry_nbtor_other	0.071
r_chiral_restr	0.038
r_bond_refined_d	0.002
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	2290
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	43

Software

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