4OT5

Crystal structure of BTK kinase domain complexed with 4-tert-Butyl-N-(3-{8-[4-(4-methyl-piperazine-1-carbonyl)-phenylamino]-imidazo[1,2-a]pyrazin-6-yl}-phenyl)-benzamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PIXPDB ENTRY 3PIX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829333% PEG3350, 0.1 M HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2545.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.768α = 90
b = 106.056β = 90
c = 38.38γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.0ALS5.0.2

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
11.554098.40.07816.44.94261719.8
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)
11.551.5985.20.3812.63.22705

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 SYNTHESISTHROUGHOUTPDB ENTRY 3PIX1.5538.3840425213898.110.143190.140530.19352RANDOM23.188
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]
0.390.6-0.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.604
r_sphericity_free27.993
r_dihedral_angle_4_deg13.507
r_dihedral_angle_3_deg11.913
r_sphericity_bonded10.764
r_rigid_bond_restr7.004
r_dihedral_angle_1_deg5.931
r_long_range_B_refined4.149
r_scbond_it3.959
r_mcangle_it2.331
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.604
r_sphericity_free27.993
r_dihedral_angle_4_deg13.507
r_dihedral_angle_3_deg11.913
r_sphericity_bonded10.764
r_rigid_bond_restr7.004
r_dihedral_angle_1_deg5.931
r_long_range_B_refined4.149
r_scbond_it3.959
r_mcangle_it2.331
r_mcbond_it2.043
r_angle_refined_deg1.908
r_chiral_restr0.157
r_bond_refined_d0.021
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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_it
r_scangle_other
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2139
Nucleic Acid Atoms
Solvent Atoms301
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing