☰ Navigation Tabs
Crystal structure of human RIP3 kinase domain complexed with LK01003
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7MX3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2 M magnesium chloride, 22.5% (w/v) polyethylene glycol 3350, 0.1 M Tris, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.48 50.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.203 α = 90 b = 129.203 β = 90 c = 79.429 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 2024-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.97918 SSRF BL10U2
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 2.93 111.89 100 0.2 0.206 0.046 0.999 11.4 20.4 16341
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 2.93 3.09 100 4.233 4.338 0.946 0.504 20.9
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.93 55.95 1.35 16250 810 99.57 0.2613 0.2584 0.3186 0.3066
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 12.409 f_angle_d 0.795 f_chiral_restr 0.047 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4478 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 62
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing