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Structure of TRIM8 RING domain in complex with UBE2N~Ub conjugate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZJ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 20% PEG3350, 0.2 M Calcium acetate hydrate
Crystal Properties Matthews coefficient Solvent content 2.33 47.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.455 α = 90 b = 177.445 β = 97.771 c = 75.592 γ = 90
Symmetry Space Group P 1 21 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 EIGER2 XE 16M 2025-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.39 49 99.7 0.193 0.076 0.98 6.2 6.3 50697 51.48
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.39 2.47 96.6 2.4 0.98 0.36 0.9 5.8
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 2.39 49 1.34 50582 2605 99.55 0.2042 0.2016 0.2017 0.2534 0.2534 58.44
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 19.6907 f_angle_d 0.835 f_chiral_restr 0.0518 f_plane_restr 0.0067 f_bond_d 0.0043
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9693 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement Aimless data scaling DIALS data scaling PHASER phasing