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Crystal structure of the kinase domain of Bruton's Tyrosine kinase with GDC0834
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OCS pdb code 3OCS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 286 1 uL protein solution (8.1 mg/mL in 10 mM Tris pH 8.5, 100 mM NaCl, 0.5 mM TCEP, 1 mM GDC0834) and 1 uL reservoir solution of 14% PEG 4000, 0.2 M Ammonium Sulfate, 0.1 M Na Acetate-Acetate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 286K
Crystal Properties Matthews coefficient Solvent content 2.26 45.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.507 α = 90 b = 108.507 β = 90 c = 42.221 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 CCD ADSC QUANTUM 210 2007-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97787 ALS 5.0.1
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 1.95 50 99.7 0.116 14.7 5.5 20873 20873 -3
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) 1 1.95 2.02 99.3 0.49 3.3 5.5 2076
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 code 3OCS 1.95 46.98 20861 20861 1053 99.65 0.16721 0.16533 0.1663 0.20251 0.2034 RANDOM 21.566
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] 0.32 0.16 0.32 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.449 r_dihedral_angle_4_deg 14.351 r_dihedral_angle_3_deg 12.579 r_dihedral_angle_1_deg 5.781 r_angle_refined_deg 1.464 r_chiral_restr 0.149 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2158 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 58
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling