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Crystal structure of a superbinder Src SH2 domain (sSrcF) in complex with a high affinity phosphopeptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F5A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 293 80 uM Zinc Acetate, 12% PEG3350, 100 mM Sodium Acetate (pH 4.0), and 2% 1,3-butanediol
Crystal Properties Matthews coefficient Solvent content 2.13 42.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.87 α = 75.85 b = 35.89 β = 74.77 c = 53.98 γ = 61.42
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 mirrors 2018-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.6 51.57 86.3 0.111 0.989 4.9 2.1 5824 53.32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.72 88.7 0.286 0.919 2.6 2.1
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 FREE R-VALUE 4F5A 2.65 51.57 1.98 5476 547 85.82 0.2237 0.2184 0.2182 0.2702 0.2687 56.06
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 16.7025 f_angle_d 1.0334 f_chiral_restr 0.0493 f_bond_d 0.0072 f_plane_restr 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1773 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction Aimless data scaling PHASER phasing