5U9D

Discovery of a potent BTK inhibitor with a novel binding mode using parallel selections with a DNA-encoded chemical library

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	Polyethylene glycols (PEG3350 / PEG5000MME), (NH4)2SO4 and MES buffer at pH6.0-6.7

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.553	α = 90
b = 103.483	β = 90
c = 37.839	γ = 90

Symmetry
Space Group	P 21 21 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 2M		2016-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00000	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.33	58.85	99.7	23.8	7.9		65295

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	1.33	1.538	99.5		0.434	5.03	7.7

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	NONE	1.33	58.85	58769	6526	99.74	0.1514	0.1484	0.1783	RANDOM	16.333

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]
0.65			-0.39		-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.696
r_sphericity_free	28.923
r_dihedral_angle_4_deg	12.966
r_dihedral_angle_3_deg	12.437
r_sphericity_bonded	7.325
r_dihedral_angle_1_deg	6.333
r_angle_other_deg	2.942
r_rigid_bond_restr	1.537
r_angle_refined_deg	1.41
r_chiral_restr	0.093

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.696
r_sphericity_free	28.923
r_dihedral_angle_4_deg	12.966
r_dihedral_angle_3_deg	12.437
r_sphericity_bonded	7.325
r_dihedral_angle_1_deg	6.333
r_angle_other_deg	2.942
r_rigid_bond_restr	1.537
r_angle_refined_deg	1.41
r_chiral_restr	0.093
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.006
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2214
Nucleic Acid Atoms
Solvent Atoms	339
Heterogen Atoms	61

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.