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Crystal structure of a superbinder Fes SH2 domain (sFes1) in complex with a high affinity phosphopeptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BKB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 2.4 M Sodium Malonate (pH 5.5) and 2% PEG300
Crystal Properties Matthews coefficient Solvent content 2.97 58.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.08 α = 90 b = 66.08 β = 90 c = 58.89 γ = 120
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 2019-06-09 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 1.25 58.89 100 0.171 0.996 10.2 11.2 40953 12.05
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 1.25 1.27 100 2.141 0.463 2.4 11.2
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 3BKB 1.25 57.23 1.34 40391 1985 99.91 0.153 0.1517 0.1511 0.1781 0.1788 18.56
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 9.348 f_angle_d 1.0822 f_chiral_restr 0.0739 f_plane_restr 0.0089 f_bond_d 0.0078
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 867 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 18
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction Aimless data scaling PHASER phasing