8ATB | pdb_00008atb

Discovery of IRAK4 Inhibitor 16

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.9	293	0.1M sodium acetate buffer, 2.13-2.145M sodium malonate

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.2	α = 90
b = 117.5	β = 90
c = 136.6	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 PILATUS 6M		2013-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

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	2.34	48.95	99.8	0.095	0.999	16.25	5.9		178315

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.34	2.48	99.6		0.83	0.805

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	inhouse structure	2.35	48.893	29596	888	99.865	0.214	0.2123	0.22	0.2601	0.26	55.616

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]
-1.049			2.564		-1.516

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.695
r_dihedral_angle_4_deg	20.318
r_dihedral_angle_3_deg	14.809
r_lrange_it	7.105
r_lrange_other	7.095
r_dihedral_angle_1_deg	5.449
r_scangle_it	4.188
r_scangle_other	4.187
r_mcangle_it	3.813
r_mcangle_other	3.813
r_scbond_it	2.379
r_scbond_other	2.379
r_mcbond_it	2.187
r_mcbond_other	2.186
r_angle_refined_deg	1.157
r_angle_other_deg	1.052
r_nbd_refined	0.164
r_symmetry_nbd_other	0.161
r_nbd_other	0.154
r_nbtor_refined	0.148
r_symmetry_xyhbond_nbd_refined	0.11
r_xyhbond_nbd_refined	0.105
r_symmetry_nbd_refined	0.105
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.036
r_gen_planes_refined	0.003
r_bond_refined_d	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	4416
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms	76

Software

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