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Crystal structure of the intertwined dimer of the c-Src tyrosine kinase SH3 domain mutant Q128K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JZ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 298 0.1M sodium acetate, 1.8 M ammonium sulphate, 5% PEG 300, 10%Glicerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.36 47.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.862 α = 90 b = 46.862 β = 90 c = 127.849 γ = 120
Symmetry Space Group P 65 2 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 PILATUS 6M (DECTRIS) CHANNEL-CUT SI(111) + KB FOCUSING MIRRORS 2012-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2 29.39 98.6 0.056 23.4 23.4 11.7 6002 36.96
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.06 96.3 0.53 4.9 11.5
Refinement Statistics Diffraction ID Structure Solution Method Starting model 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 4JZ4 2 29.39 1.54 5977 466 98.2 0.238 0.236 0.2468 0.261 0.2621 46.46
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 14.215 f_angle_d 1.141 f_chiral_restr 0.046 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 453 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 17
Software Software Software Name Purpose Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction XDS data reduction