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TRIM21-NUP98 Molecular Glue Complex (MAN-021)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other 056 model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 100 mM NaCl, 100 mM HEPES, pH 7.5, 12 % polyethylene glycol 20,000
Crystal Properties Matthews coefficient Solvent content 2.46 49.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.978 α = 90 b = 71.495 β = 90 c = 97.195 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 PIXEL DECTRIS EIGER2 XE 16M 2025-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.979460 SSRL BL12-2
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 1.2 49.18 74.2 0.065 12.3 6 92180
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 0.787
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 1.32 49.18 84004 4233 89.494 0.152 0.1503 0.1509 0.1781 0.1771 17.437
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] 2.242 -1.006 -1.236
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.947 r_dihedral_angle_3_deg 11.713 r_dihedral_angle_2_deg 9.23 r_lrange_it 8.556 r_lrange_other 8.555 r_dihedral_angle_1_deg 6.823 r_scangle_it 4.198 r_scangle_other 4.197 r_scbond_it 2.761 r_scbond_other 2.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.947 r_dihedral_angle_3_deg 11.713 r_dihedral_angle_2_deg 9.23 r_lrange_it 8.556 r_lrange_other 8.555 r_dihedral_angle_1_deg 6.823 r_scangle_it 4.198 r_scangle_other 4.197 r_scbond_it 2.761 r_scbond_other 2.76 r_mcangle_other 2.127 r_mcangle_it 2.125 r_angle_refined_deg 1.911 r_mcbond_it 1.397 r_mcbond_other 1.397 r_angle_other_deg 0.658 r_symmetry_xyhbond_nbd_refined 0.301 r_symmetry_nbd_refined 0.292 r_xyhbond_nbd_refined 0.244 r_nbd_other 0.235 r_nbd_refined 0.23 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.186 r_chiral_restr 0.106 r_symmetry_nbtor_other 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 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 463 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHENIX phasing