☰ Navigation Tabs
Crystal Structure of Hck in complex with the Src-family kinase inhibitor A-419259
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QCF SH3, SH2, SH1, separated, single search models
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 10 mM Tris-HCl, pH 8.3, 75 mM NaCl, 5% glycerol, 2 mM TCEP, 0.1 M sodium thiocyanate, 10% w/v PEG 3350, 0.095 mM 7-[trans-4-(4-Methyl-1-piperazinyl)cyclohexyl]-5-(4-phenoxyphenyl)-7H-Pyrrolo[2,3-d]pyrimidin-4-amine, 0.5 mM N~2~-{[2-(2,4-difluorophenoxy)pyridin-3-yl]methyl}-N~4~-isopropylpyrimidine-2,4-diamine,1 % DMSO
Crystal Properties Matthews coefficient Solvent content 2.32 47.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.346 α = 90 b = 85.025 β = 90 c = 128.798 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2020-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03317 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.8 42.5125 99.95 0.148 0.16 0.998 8.5 7.1 44990 33.27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 99.64 2.898 3.135 0.301 0.6 6.97
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 1.8 42.51 1.34 42703 3764 99.12 0.2003 0.1994 0.1994 0.2192 0.2192 45.67
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 16.7316 f_angle_d 1.6009 f_chiral_restr 0.0967 f_plane_restr 0.0301 f_bond_d 0.0149
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3580 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 113
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection XDS data reduction PHASER phasing Coot model building XSCALE data scaling