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Crystal structure of the intertwined form of the Src tyrosine kinase SH3 domain E97T-Q128R mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JZ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 0.1M sodium acetate, 2.2 M ammonium sulphate, 10 %PEG 300, 10% Glycerol
Crystal Properties Matthews coefficient Solvent content 3.05 59.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.29 α = 90 b = 46.29 β = 90 c = 126.55 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 MARMOSAIC 225 mm CCD 2015-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97872 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 19.8 97.6 0.073 0.021 0.999 24.3 13.4 4990 35.17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 96.6 0.749 0.204 0.889 3.9 14.1 379
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4JZ3 2.1 19.797 0.84 4987 458 97.68 0.2116 0.2103 0.2173 0.2332 0.2165 Random selection 47.6281
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 13.685 f_angle_d 1.299 f_chiral_restr 0.056 f_bond_d 0.012 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 429 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 39
Software Software Software Name Purpose iMOSFLM data reduction Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction