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TRIM21-NUP98 Molecular Glue Complex (MAN-056)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q5Y in silico model AlphaFold AF-P19474-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 100 mM NaCl, 100 mM HEPES, pH 7.5, 12 % polyethylene glycol 20,000
Crystal Properties Matthews coefficient Solvent content 2.48 50.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.481 α = 90 b = 71.307 β = 90 c = 97.455 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 99.5 PIXEL DECTRIS EIGER2 XE 16M 2025-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.979460 SSRL BL12-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.56 49.51 99.4 0.128 7.4 6.1 57407
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 1.56 1.6 0.344
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.6 49.51 52315 2608 97.617 0.177 0.1748 0.1848 0.2137 0.2193 22.846
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] 2.205 -0.844 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.058 r_dihedral_angle_6_deg 15.94 r_dihedral_angle_3_deg 11.872 r_lrange_other 7.348 r_lrange_it 7.347 r_dihedral_angle_1_deg 6.975 r_scangle_it 4.894 r_scangle_other 4.893 r_scbond_it 3.139 r_scbond_other 3.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.058 r_dihedral_angle_6_deg 15.94 r_dihedral_angle_3_deg 11.872 r_lrange_other 7.348 r_lrange_it 7.347 r_dihedral_angle_1_deg 6.975 r_scangle_it 4.894 r_scangle_other 4.893 r_scbond_it 3.139 r_scbond_other 3.138 r_mcangle_other 2.51 r_mcangle_it 2.504 r_mcbond_it 1.693 r_angle_refined_deg 1.692 r_mcbond_other 1.692 r_angle_other_deg 0.594 r_symmetry_xyhbond_nbd_refined 0.353 r_symmetry_nbd_refined 0.255 r_xyhbond_nbd_refined 0.249 r_nbd_other 0.228 r_nbd_refined 0.212 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.183 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.087 r_chiral_restr_other 0.033 r_symmetry_xyhbond_nbd_other 0.017 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2671 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHENIX phasing