4OTF

Crystal structure of the kinase domain of Bruton's Tyrosine kinase with GDC0834


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OCSpdb code 3OCS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62861 uL protein solution (8.1 mg/mL in 10 mM Tris pH 8.5, 100 mM NaCl, 0.5 mM TCEP, 1 mM GDC0834) and 1 uL reservoir solution of 14% PEG 4000, 0.2 M Ammonium Sulfate, 0.1 M Na Acetate-Acetate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 286K
Crystal Properties
Matthews coefficientSolvent content
2.2645.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.507α = 90
b = 108.507β = 90
c = 42.221γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102007-10-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.97787ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.955099.70.11614.75.52087320873-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0299.30.493.35.52076

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb code 3OCS1.9546.982086120861105399.650.167210.165330.20251RANDOM21.566
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]
0.320.160.32-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.449
r_dihedral_angle_4_deg14.351
r_dihedral_angle_3_deg12.579
r_dihedral_angle_1_deg5.781
r_angle_refined_deg1.464
r_chiral_restr0.149
r_bond_refined_d0.008
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2158
Nucleic Acid Atoms
Solvent Atoms182
Heterogen Atoms58

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling