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Crystal Structure of 5-(trifluoromethoxy)indoline-2,3-dione covalently bound to the PH domain of Bruton's tyrosine kinase mutant R28C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BTK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.1 M TRIS 8.5 pH, 32.5% w/v PEG 3350, 200mM MgCl2 500 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.27 45.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.649 α = 90 b = 67.195 β = 99.66 c = 79.641 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS 6M 2017-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9797 Diamond I24
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 1.95 51.06 100 0.145 0.152 0.046 0.997 8.6 10.8 52358
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 1.95 2 100 2.336 2.474 0.803 0.648 9.4
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 1BTK 1.95 51.05 49164 2575 98.78 0.2338 0.2304 0.2433 0.2988 0.3039 RANDOM 41.561
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] 1.69 -0.35 1.88 -3.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.527 r_dihedral_angle_3_deg 18.178 r_dihedral_angle_4_deg 16.807 r_dihedral_angle_1_deg 8.263 r_angle_refined_deg 1.588 r_angle_other_deg 1.22 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.527 r_dihedral_angle_3_deg 18.178 r_dihedral_angle_4_deg 16.807 r_dihedral_angle_1_deg 8.263 r_angle_refined_deg 1.588 r_angle_other_deg 1.22 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5206 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction