3K54 | pdb_00003k54

Structures of human Bruton's tyrosine kinase in active and inactive conformations suggests a mechanism of activation for TEC family kinases.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1K2P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	273	20% Peg5000 MME, 0.2M Ammonium Acetate, 0.1M Bis-Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.438	α = 90
b = 104.622	β = 90
c = 38.107	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	CCD	RAYONIX MX-225	Monochromator: Kohzu HLD-4 Double Crystal	2009-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.98	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.94	50	99.2	0.083	32	6.8	22496	21816	2	3.3	29.9

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	1.94	2.01	99.2		0.619	3.31	6.6	2198

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1K2P	1.94	28.4	2	21141	1125	99.16	0.20184	0.1989	0.2	0.25813	0.26	RANDOM	24.651

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]
0.3			-0.44		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.602
r_dihedral_angle_4_deg	21.003
r_dihedral_angle_3_deg	18.345
r_dihedral_angle_1_deg	6.506
r_scangle_it	5.21
r_scbond_it	3.276
r_mcangle_it	2.244
r_angle_refined_deg	2.045
r_mcbond_it	1.295
r_chiral_restr	0.189

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.602
r_dihedral_angle_4_deg	21.003
r_dihedral_angle_3_deg	18.345
r_dihedral_angle_1_deg	6.506
r_scangle_it	5.21
r_scbond_it	3.276
r_mcangle_it	2.244
r_angle_refined_deg	2.045
r_mcbond_it	1.295
r_chiral_restr	0.189
r_bond_refined_d	0.024
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2008
Nucleic Acid Atoms
Solvent Atoms	164
Heterogen Atoms	33

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling

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 R01GM157729.