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Crystal structure of the mouse RIP3 kinase domain in complexed with GSK'872
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4M66
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 10-20% PEG3350, 50 mM magnesium formate, pH 5.0-7.5
Crystal Properties Matthews coefficient Solvent content 1.96 37.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.312 α = 90 b = 48.904 β = 131.33 c = 103.382 γ = 90
Symmetry Space Group C 1 2 1
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 6M 2019-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97930 SSRF BL18U1
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 1.93 50 99.9 0.083 0.09 0.035 0.993 4.6 6.6 42598
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 1.93 1.96 100 0.654 0.709 0.272 0.862 6.6
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 4M66 1.93 23.84 1.36 42581 1983 99.79 0.1826 0.1813 0.1818 0.2087 0.2098
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 14.938 f_angle_d 0.8 f_chiral_restr 0.049 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4362 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement HKL-3000 data scaling HKL-3000 data reduction HKL-3000 phasing