6YYK

Crystal Structure of 1,5-dimethylindoline-2,3-dione covalently bound to the PH domain of Bruton's tyrosine kinase mutant R28C

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	0.1 M TRIS 8.5 pH, 32.5% w/v PEG 3350, 200mM MgCl2 500 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.199	α = 90
b = 60.344	β = 96.57
c = 58.058	γ = 90

Symmetry
Space Group	P 1 21 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		2017-04-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2.04	60.41	99.8	0.074	0.09	0.049	0.996	5.3	3.2		21231

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.04	2.09	99.6		1.346	1.637	0.921	0.661		3

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	1BTK	2.04	57.74	19781	1021	97.49	0.2307	0.2275	0.2964	RANDOM	67.47

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]
3.05		8.03	-4.47		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.961
r_dihedral_angle_3_deg	18.14
r_dihedral_angle_4_deg	12.73
r_dihedral_angle_1_deg	7.724
r_angle_refined_deg	1.563
r_angle_other_deg	1.207
r_chiral_restr	0.071
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.961
r_dihedral_angle_3_deg	18.14
r_dihedral_angle_4_deg	12.73
r_dihedral_angle_1_deg	7.724
r_angle_refined_deg	1.563
r_angle_other_deg	1.207
r_chiral_restr	0.071
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2631
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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.