3K54

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)
TypeSourceAccession CodeDetails
experimental modelPDB 1K2P 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.527320% Peg5000 MME, 0.2M Ammonium Acetate, 0.1M Bis-Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
2.2445.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.438α = 90
b = 104.622β = 90
c = 38.107γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-225Monochromator: Kohzu HLD-4 Double Crystal2009-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.98APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.945099.20.083326.8224962181623.329.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.942.0199.20.6193.316.62198

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1K2P1.9428.4221141112599.160.201840.19890.25813RANDOM24.651
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]
0.3-0.440.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.602
r_dihedral_angle_4_deg21.003
r_dihedral_angle_3_deg18.345
r_dihedral_angle_1_deg6.506
r_scangle_it5.21
r_scbond_it3.276
r_mcangle_it2.244
r_angle_refined_deg2.045
r_mcbond_it1.295
r_chiral_restr0.189
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.602
r_dihedral_angle_4_deg21.003
r_dihedral_angle_3_deg18.345
r_dihedral_angle_1_deg6.506
r_scangle_it5.21
r_scbond_it3.276
r_mcangle_it2.244
r_angle_refined_deg2.045
r_mcbond_it1.295
r_chiral_restr0.189
r_bond_refined_d0.024
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2008
Nucleic Acid Atoms
Solvent Atoms164
Heterogen Atoms33

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling