8BR6 | pdb_00008br6

Discovery of IRAK4 Inhibitor 40

X-RAY DIFFRACTION

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Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.725	α = 90
b = 118.573	β = 90
c = 138.709	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		2013-12-11	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	2.167	46.303	99.7	0.138	0.998	10.85	5.01		38659

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			0.651	1.71

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	THROUGHOUT	in house model	2.167	46.303	38633	1932	99.634	0.215	0.2133	0.22	0.2513	0.25	48.702

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]
-0.289			2.981		-2.692

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.548
r_dihedral_angle_4_deg	22.357
r_dihedral_angle_3_deg	14.796
r_lrange_other	9.356
r_lrange_it	9.351
r_scangle_it	7.29
r_scangle_other	7.289
r_dihedral_angle_1_deg	6.009
r_mcangle_it	5.77
r_mcangle_other	5.769
r_scbond_it	4.251
r_scbond_other	4.25
r_mcbond_it	3.577
r_mcbond_other	3.576
r_angle_refined_deg	1.22
r_angle_other_deg	1.107
r_nbd_other	0.172
r_nbd_refined	0.171
r_symmetry_nbd_other	0.167
r_symmetry_nbd_refined	0.167
r_symmetry_xyhbond_nbd_refined	0.163
r_nbtor_refined	0.151
r_xyhbond_nbd_refined	0.119
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.043
r_xyhbond_nbd_other	0.014
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4440
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms	64

Software

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