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Crystal structure of BTK kinase domain complexed with 4-Methanesulfonyl-N-(3-{8-[4-(morpholine-4-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 2.23 44.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.825 α = 90 b = 105.389 β = 90 c = 38.24 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 2.05 42.49 95.7 0.245 4.8 4.1 18568 32.4
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 2.05 2.1 95.97 0.882 1.81 2.5
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 2.05 42.49 17497 950 97.52 0.21936 0.21607 0.2174 0.27788 0.2798 RANDOM 39.922
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] -3.04 5.01 -1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.134 r_dihedral_angle_4_deg 20.72 r_dihedral_angle_3_deg 14.303 r_long_range_B_refined 6.949 r_dihedral_angle_1_deg 6.129 r_scbond_it 2.887 r_mcangle_it 2.6 r_mcbond_it 1.806 r_angle_refined_deg 1.436 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.134 r_dihedral_angle_4_deg 20.72 r_dihedral_angle_3_deg 14.303 r_long_range_B_refined 6.949 r_dihedral_angle_1_deg 6.129 r_scbond_it 2.887 r_mcangle_it 2.6 r_mcbond_it 1.806 r_angle_refined_deg 1.436 r_chiral_restr 0.098 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2159 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement CNS refinement ADSC data collection DENZO data reduction SCALEPACK data scaling CNS phasing