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Crystal structure of BTK kinase domain bound to a tirabrutinib analog with an acrylamide 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 5.6 277 20% PEG4000, 0.1M Sodium Citrate
Crystal Properties Matthews coefficient Solvent content 2.44 48.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.554 α = 90 b = 106.554 β = 90 c = 46.383 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 2.48 53.28 100 0.15 0.154 0.035 0.998 13.6 16.8 20727
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.489 2.497 100 1.236 1.426 0.701 0.379 1.5 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 2.48 53.28 1.96 20727 1082 98.82 0.2405 0.2334 0.2374 0.2814 0.2853 88.07
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 12.8447 f_angle_d 0.6158 f_chiral_restr 0.0408 f_plane_restr 0.0046 f_bond_d 0.0025
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4003 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 66
Software Software Software Name Purpose PHENIX refinement PHASER phasing autoPROC data processing Coot model building XDS data reduction XDS data scaling