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Intertwined dimer of the PTK6 SH3 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JT9 experimental model PDB 6NMW experimental model PDB 2HDA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 293 2.5 M Sodium chloride
100 mM Sodium Potassium phosphate; pH 6.2
Crystal Properties Matthews coefficient Solvent content 2.53 51.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.17 α = 90 b = 42.75 β = 90 c = 94.86 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 S 2M 2023-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.75 38.53 84.5 0.88 18.8 13.7 16795 23.72
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.813 82.01 0.92
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.75 38.53 0.04 16788 842 93.48 0.1954 0.194 0.194 0.2226 0.2225 29.92
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 13.2196 f_angle_d 0.9303 f_chiral_restr 0.057 f_plane_restr 0.011 f_bond_d 0.0087
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 970 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHENIX phasing