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Crystal structure of BTK kinase domain bound to an ibrutinib analog with a 2-butynamide warhead
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5P9J experimental model PDB 5P9M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 25% PEG3350, 0.1M bis-Tris, 0.2M ammonium sulfate.
Crystal Properties Matthews coefficient Solvent content 2.46 50.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.593 α = 90 b = 107.593 β = 90 c = 45.955 γ = 120
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 2025-06-24 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 2.434 93.178 93.178 0.141 0.127 0.049 0.928 9.7 8.1 10423 64.88
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.434 2.549 35.4 2.402 2.585 0.947 1.2 7.4
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 2.48 53.8 1.36 10360 482 94.42 0.212 0.2106 0.2116 0.2414 0.2404 74.45
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 15.0133 f_angle_d 0.8733 f_chiral_restr 0.0502 f_plane_restr 0.008 f_bond_d 0.0043
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2052 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 34
Software Software Software Name Purpose PHENIX refinement XDS data scaling autoPROC data processing PHASER phasing Coot model building XDS data reduction