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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
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PIX PDB ENTRY 3PIX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 33% PEG3350, 0.1 M HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.25 45.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.768 α = 90 b = 106.056 β = 90 c = 38.38 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.55 40 98.4 0.078 16.4 4.9 42617 19.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.59 85.2 0.381 2.6 3.2 2705
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 3PIX 1.55 38.38 40425 2138 98.11 0.14319 0.14053 0.141 0.19352 0.1939 RANDOM 23.188
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] 0.39 0.6 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.604 r_sphericity_free 27.993 r_dihedral_angle_4_deg 13.507 r_dihedral_angle_3_deg 11.913 r_sphericity_bonded 10.764 r_rigid_bond_restr 7.004 r_dihedral_angle_1_deg 5.931 r_long_range_B_refined 4.149 r_scbond_it 3.959 r_mcangle_it 2.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.604 r_sphericity_free 27.993 r_dihedral_angle_4_deg 13.507 r_dihedral_angle_3_deg 11.913 r_sphericity_bonded 10.764 r_rigid_bond_restr 7.004 r_dihedral_angle_1_deg 5.931 r_long_range_B_refined 4.149 r_scbond_it 3.959 r_mcangle_it 2.331 r_mcbond_it 2.043 r_angle_refined_deg 1.908 r_chiral_restr 0.157 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 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 Atoms Number Protein Atoms 2139 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement CNS refinement ADSC data collection DENZO data reduction SCALEPACK data scaling CNS phasing