8BR5 | pdb_00008br5

Discovery of IRAK4 Inhibitor 41

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	none

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.214	α = 90
b = 141.199	β = 124.458
c = 87.919	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		2017-08-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000	SLS	X10SA

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	2.7	90.583	99.3	0.094	0.998	16.8	4.42		39488

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	2.7	2.95			0.523	0.882	3.58

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	2.7	90.583	39488	746	99.752	0.215	0.2146	0.22	0.2541	0.26	57.762

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]
3.186		1.988	-4.382		-0.789

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.178
r_dihedral_angle_4_deg	20.156
r_dihedral_angle_3_deg	15.496
r_lrange_it	12.203
r_lrange_other	12.203
r_scangle_it	9.176
r_scangle_other	9.175
r_mcangle_it	7.673
r_mcangle_other	7.672
r_scbond_it	5.624
r_scbond_other	5.623
r_dihedral_angle_1_deg	4.933
r_mcbond_it	4.891
r_mcbond_other	4.891
r_angle_refined_deg	1.253
r_angle_other_deg	1.069
r_symmetry_xyhbond_nbd_refined	0.435
r_nbd_other	0.215
r_symmetry_nbd_refined	0.194
r_symmetry_nbd_other	0.174
r_nbd_refined	0.168
r_nbtor_refined	0.149
r_xyhbond_nbd_refined	0.141
r_ncsr_local_group_2	0.12
r_ncsr_local_group_6	0.118
r_ncsr_local_group_4	0.112
r_ncsr_local_group_5	0.109
r_ncsr_local_group_1	0.107
r_ncsr_local_group_3	0.107
r_xyhbond_nbd_other	0.103
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.041
r_symmetry_xyhbond_nbd_other	0.029
r_chiral_restr_other	0.022
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9039
Nucleic Acid Atoms
Solvent Atoms	145
Heterogen Atoms	116

Software

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