6EP9

Crystal structure of BTK kinase domain complexed with N-[2-methyl-3-[4-methyl-6-[4-(4-methylpiperazine-1-carbonyl)anilino]-5-oxo-pyrazin-2-yl]phenyl]-4-(1-piperidyl)benzamide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829333% PEG3350, 0.1M HEPES
Crystal Properties
Matthews coefficientSolvent content
2.2745.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.408α = 90
b = 106.948β = 90
c = 38.126γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-05-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.97946SSRLBL9-1

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
124092.30.10410.14.218672
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)
122.0252.20.4451.72.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.0138.121768894991.180.200830.198750.23916RANDOM30.96
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]
3.02-1.34-1.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.698
r_dihedral_angle_4_deg14.239
r_dihedral_angle_3_deg11.873
r_dihedral_angle_1_deg5.401
r_scangle_it1.689
r_scbond_it1.074
r_angle_refined_deg1.041
r_mcangle_it0.75
r_mcbond_it0.484
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.698
r_dihedral_angle_4_deg14.239
r_dihedral_angle_3_deg11.873
r_dihedral_angle_1_deg5.401
r_scangle_it1.689
r_scbond_it1.074
r_angle_refined_deg1.041
r_mcangle_it0.75
r_mcbond_it0.484
r_nbtor_refined0.303
r_symmetry_hbond_refined0.201
r_nbd_refined0.183
r_symmetry_vdw_refined0.165
r_xyhbond_nbd_refined0.132
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
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
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2139
Nucleic Acid Atoms
Solvent Atoms189
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction