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Fragment-Based Discovery of a Small Molecule Reversible Inhibitor of Bruton's Tyrosine Kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GEN PDB entry 3GEN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 10% polyethylene glycol 4000, 20% glycerol, 0.1M imidazole/MES, pH 6.5, 0.12M alcohol mixture
Crystal Properties Matthews coefficient Solvent content 2.29 46.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.092 α = 90 b = 104.1 β = 90 c = 38.078 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 MARMOSAIC 300 mm CCD 2012-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.55 50 95 0.097 9.5 6.5 40885
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3GEN 1.6 30 36431 1914 97.76 0.1663 0.1646 0.1647 0.1975 0.1973 RANDOM 17.847
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] 1.05 -0.47 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.866 r_dihedral_angle_4_deg 15.597 r_dihedral_angle_3_deg 11.778 r_dihedral_angle_1_deg 6.462 r_angle_refined_deg 1.286 r_chiral_restr 0.107 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2214 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 42
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction