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Crystal structure of BTK kinase domain complexed with 3-(2,6-Dichloro-phenyl)-7-[4-(2-diethylamino-ethoxy)-phenylamino]-1-methyl-3,4-dihydro-1H-pyrimido[4,5-d]pyrimidin-2-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 2.25 45.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.728 α = 90 b = 104.818 β = 90 c = 38.17 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 0.9804 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 2 40 99.6 0.135 13.2 6.9 20034
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) 2 2.07 96.8 0.393 2.8 2.1 1881
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 40 18971 1019 99.4 0.22323 0.22147 0.2215 0.25685 0.2566 RANDOM 24.717
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] 0.31 -0.51 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.176 r_dihedral_angle_4_deg 14.764 r_dihedral_angle_3_deg 14.289 r_dihedral_angle_1_deg 5.174 r_scangle_it 1.828 r_scbond_it 1.137 r_mcangle_it 1.024 r_angle_refined_deg 0.976 r_mcbond_it 0.615 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.176 r_dihedral_angle_4_deg 14.764 r_dihedral_angle_3_deg 14.289 r_dihedral_angle_1_deg 5.174 r_scangle_it 1.828 r_scbond_it 1.137 r_mcangle_it 1.024 r_angle_refined_deg 0.976 r_mcbond_it 0.615 r_nbtor_refined 0.304 r_nbd_refined 0.175 r_symmetry_vdw_refined 0.174 r_symmetry_hbond_refined 0.171 r_xyhbond_nbd_refined 0.114 r_chiral_restr 0.071 r_bond_refined_d 0.007 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 1977 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 62
Software Software Software Name Purpose ADSC data collection REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing