3GEN

The 1.6 A crystal structure of human bruton's tyrosine kinase bound to a pyrrolopyrimidine-containing compound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1K2P 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.527730% Peg MME 5000,0.2M Ammonium Sulfate, 0.1M MES pH 6.5 , VAPOR DIFFUSION, SITTING DROP, temperature 277.0K
Crystal Properties
Matthews coefficientSolvent content
2.244.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.497α = 90
b = 104.306β = 90
c = 38.039γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKUVarimax HR optics2008-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-D1.54

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
11.624.598.10.083.83820622
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)
1.61.6698.50.3634.1

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 REPLACEMENTTHROUGHOUT1K2P1.621.933629336291191598.130.19460.192610.23168RANDOM28.639
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.97
r_dihedral_angle_4_deg14.041
r_dihedral_angle_3_deg12.911
r_dihedral_angle_1_deg5.471
r_mcbond_other2.876
r_scangle_it2.39
r_scbond_it1.739
r_sphericity_free1.677
r_rigid_bond_restr1.661
r_sphericity_bonded1.577
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.97
r_dihedral_angle_4_deg14.041
r_dihedral_angle_3_deg12.911
r_dihedral_angle_1_deg5.471
r_mcbond_other2.876
r_scangle_it2.39
r_scbond_it1.739
r_sphericity_free1.677
r_rigid_bond_restr1.661
r_sphericity_bonded1.577
r_angle_other_deg1.265
r_mcangle_it1.179
r_angle_refined_deg1.145
r_mcbond_it0.977
r_nbtor_refined0.309
r_nbd_other0.297
r_nbd_refined0.218
r_symmetry_vdw_refined0.198
r_xyhbond_nbd_refined0.186
r_symmetry_hbond_refined0.157
r_nbtor_other0.089
r_chiral_restr0.081
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.003
r_gen_planes_other0.003
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2161
Nucleic Acid Atoms
Solvent Atoms495
Heterogen Atoms28

Software

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