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Crystal structure of human Fer SH2 domain bound to a phosphopeptide (DEpYENVD)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2KK6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 293 HEPES, sodium chloride, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.15 42.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.7 α = 90 b = 186.661 β = 96.96 c = 50.58 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 95 PIXEL DECTRIS EIGER X 16M 2018-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
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 1.37 25.87 97.7 0.044 0.052 0.028 0.997 14.8 3.1 130076
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 1.37 1.39 89.8 0.116 0.143 0.082 0.981 2.8
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2KK6 1.37 25.867 1.34 129994 6701 97.64 0.1657 0.1646 0.1661 0.1855 0.1867 20.8914
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5290 Nucleic Acid Atoms Solvent Atoms 1075 Heterogen Atoms
Software Software Software Name Purpose Aimless data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction