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Crystal structure of BTK kinase domain complexed with 2-[4-(2-Diethylamino-ethoxy)-phenylamino]-6-(4-fluoro-phenoxy)-8-methyl-8H-pyrido[2,3-d]pyrimidin-7-one
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, 0.1M HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.23 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.356 α = 90 b = 104.803 β = 90 c = 38.002 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 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9795 SSRL BL9-2
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 1.75 50 92.7 0.067 15.6 3.9 27449
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) 1.75 1.81 60 0.235 2.4 2.2 1560
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 1.75 42.22 26007 1394 92.66 0.23086 0.22916 0.2292 0.26307 0.2635 RANDOM 33.022
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] 1.95 0.44 -2.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.039 r_dihedral_angle_4_deg 16.917 r_dihedral_angle_3_deg 12.515 r_dihedral_angle_1_deg 4.638 r_scangle_it 1.671 r_scbond_it 1.048 r_angle_refined_deg 0.959 r_mcangle_it 0.887 r_mcbond_it 0.542 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.039 r_dihedral_angle_4_deg 16.917 r_dihedral_angle_3_deg 12.515 r_dihedral_angle_1_deg 4.638 r_scangle_it 1.671 r_scbond_it 1.048 r_angle_refined_deg 0.959 r_mcangle_it 0.887 r_mcbond_it 0.542 r_nbtor_refined 0.304 r_nbd_refined 0.175 r_symmetry_vdw_refined 0.166 r_xyhbond_nbd_refined 0.097 r_symmetry_hbond_refined 0.095 r_chiral_restr 0.069 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2041 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 35
Software Software Software Name Purpose ADSC data collection REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing