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Crystal structure of BTK kinase domain complexed with (5-Amino-1-o-tolyl-1H-pyrazol-4-yl)-[3-(1-methanesulfonyl-piperidin-4-yl)-phenyl]-methanone
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 2.24 45.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.267 α = 90 b = 105.304 β = 90 c = 38.054 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 2.2 40 91.6 0.135 9 4 13820
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 2.28 61.8 0.278 2.3 2.1 909
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 2.21 38.04 13089 692 91.43 0.22759 0.22493 0.2231 0.28164 0.2812 RANDOM 40.375
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] 2.88 -0.42 -2.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.165 r_dihedral_angle_4_deg 23.354 r_dihedral_angle_3_deg 14.615 r_dihedral_angle_1_deg 5.215 r_scangle_it 1.904 r_scbond_it 1.185 r_angle_refined_deg 1.01 r_mcangle_it 0.968 r_mcbond_it 0.579 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.165 r_dihedral_angle_4_deg 23.354 r_dihedral_angle_3_deg 14.615 r_dihedral_angle_1_deg 5.215 r_scangle_it 1.904 r_scbond_it 1.185 r_angle_refined_deg 1.01 r_mcangle_it 0.968 r_mcbond_it 0.579 r_nbtor_refined 0.306 r_nbd_refined 0.182 r_symmetry_vdw_refined 0.161 r_xyhbond_nbd_refined 0.132 r_symmetry_hbond_refined 0.086 r_chiral_restr 0.074 r_bond_refined_d 0.008 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 2017 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 31
Software Software Software Name Purpose ADSC data collection REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing