8ATN | pdb_00008atn

Discovery of IRAK4 Inhibitor 38

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.9	293	0.1M sodium acetate buffer pH 4.9, 1.5-1.7M ammonium citrate, 0.02M hexaaminecobalt(III)chloride

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.194	α = 90
b = 118.899	β = 90
c = 140.475	γ = 90

Symmetry
Space Group	I 2 2 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		2021-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9763	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.17	49.88	99.9	0.119	0.999	13.77	13.75		39306

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.17	2.3			0.767

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	in house model	2.171	49.875	39289	1965	99.898	0.242	0.2384	0.24	0.3059	0.31	77.038

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]
-8.899			8.235		0.664

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.338
r_dihedral_angle_4_deg	25.87
r_dihedral_angle_3_deg	23.671
r_lrange_it	12.842
r_lrange_other	12.839
r_scangle_it	10.794
r_scangle_other	10.792
r_scbond_it	7.431
r_scbond_other	7.429
r_mcangle_it	7.333
r_mcangle_other	7.333
r_dihedral_angle_1_deg	6.611
r_mcbond_it	5.12
r_mcbond_other	5.116
r_angle_refined_deg	1.767
r_angle_other_deg	1.356
r_symmetry_nbd_refined	0.632
r_nbd_other	0.255
r_nbd_refined	0.228
r_symmetry_nbd_other	0.221
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.157
r_symmetry_nbtor_other	0.088
r_symmetry_xyhbond_nbd_refined	0.083
r_chiral_restr	0.073
r_symmetry_xyhbond_nbd_other	0.031
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4451
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing