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Crystal structure of human Btk SH2 domain bound to rF10 repebody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GE9 SH2 domain (Chain A) was based in an homology model generated using 2GE9, 2EU0 and 3S9K. The repebody (chain B) initial model was 5B4P experimental model PDB 2EU0 SH2 domain (Chain A) was based in an homology model generated using 2GE9, 2EU0 and 3S9K. The repebody (chain B) initial model was 5B4P experimental model PDB 3S9K SH2 domain (Chain A) was based in an homology model generated using 2GE9, 2EU0 and 3S9K. The repebody (chain B) initial model was 5B4P experimental model PDB 5B4P SH2 domain (Chain A) was based in an homology model generated using 2GE9, 2EU0 and 3S9K. The repebody (chain B) initial model was 5B4P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 Morpheus B12 BUFFER 0.09M Halogens 0,1M Buffer 3 pH 8.5 50% precipitant 4
Crystal Properties Matthews coefficient Solvent content 2 43.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.521 α = 90 b = 32.947 β = 90 c = 80.624 γ = 90
Symmetry Space Group P 21 21 2
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 2M 2018-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.102 41.564 99.7 0.102 12.99 3.89 43493
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.102 2.23 99.5 0.81 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 SH2 domain (Chain A) was based in an homology model generated using 2GE9, 2EU0 and 3S9K. The repebody (chain B) initial model was 5B4P 2.102 41.564 22065 1883 93.95 0.2144 0.2105 0.2122 0.256 0.2474
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 4.848 f_angle_d 0.889 f_chiral_restr 0.053 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2897 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing