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Structure of BTK kinase domain with the second-generation inhibitor acalabrutinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5P9J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6.5 277 20% PEG 3350, 0.1M Bis-tris propane, pH 6.5 and 0.2M sodium bromide
Crystal Properties Matthews coefficient Solvent content 2.25 45.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.921 α = 90 b = 50.31 β = 90 c = 123.483 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 S 16M 2022-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.626 46.591 82.2 0.148 0.162 0.064 0.996 1.2 5.5 28343 17.65
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.626 1.745 21.8 1.276 0.582 0.499 1.5 5.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.7 19.74 1.34 27871 1394 92.25 0.1887 0.1866 0.1865 0.2276 0.2272 23.15
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.0686 f_angle_d 0.4745 f_chiral_restr 0.0388 f_plane_restr 0.0032 f_bond_d 0.0016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2215 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 39
Software Software Software Name Purpose PHENIX refinement autoPROC data processing PHASER phasing autoPROC data reduction XDS data scaling Coot model building