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Crystal structure of the T98D c-Src-SH3 domain mutant in complex with the high affinity peptide APP12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FJ5 PDB entry 3FJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 1.7 M Ammonium sulphate, 10% PEG 300, 10% glycerol and 0.1 M sodium acetate, pH 5, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.89 34.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.503 α = 90 b = 31.503 β = 90 c = 106.71 γ = 120
Symmetry Space Group P 31 2 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 vertical focusing mirror (VFM) and a horizontal focusing mirror(HFM), manufactured by IRELEC. 2012-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97951 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 0.98 35.57 97.9 0.037 29.5 4.8 36286 35524 10.023
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 0.98 1 82.8 0.169 3.9 1.8 1418
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 entry 3FJ5 0.98 19.074 1.44 68001 64397 3221 94.7 0.1456 0.1456 0.1449 0.1482 0.16 0.1592 RANDOM 18.5467
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 11.022 f_angle_d 1.551 f_chiral_restr 0.086 f_bond_d 0.011 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 544 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 11
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction ADSC data collection XDS data reduction PHASER phasing