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Human TRIM21 PRYSPRY domain in complex with compound 5 (Z31)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9QBA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.5 293 2.3 M Sodium Chloride
0.1 M Sodium Citrate
Crystal Properties Matthews coefficient Solvent content 2.15 42.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.593 α = 90 b = 64.593 β = 90 c = 73.527 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 EIGER2 XE 16M 2025-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 1.5 55.94 100 0.05 0.052 0.011 1 29.5 20.8 27917
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 1.5 1.53 99.7 1.079 1.106 0.239 0.865 20.9
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.5 55.94 26530 1353 99.99 0.16511 0.16352 0.1733 0.19636 0.2032 RANDOM 25.531
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] 0.36 0.18 0.36 -1.15
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 13.647 r_long_range_B_other 13.645 r_dihedral_angle_3_deg 12.246 r_mcangle_it 9.544 r_mcangle_other 9.544 r_scangle_other 9.183 r_dihedral_angle_1_deg 7.279 r_mcbond_it 6.52 r_mcbond_other 6.495 r_scbond_it 6.273
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 13.647 r_long_range_B_other 13.645 r_dihedral_angle_3_deg 12.246 r_mcangle_it 9.544 r_mcangle_other 9.544 r_scangle_other 9.183 r_dihedral_angle_1_deg 7.279 r_mcbond_it 6.52 r_mcbond_other 6.495 r_scbond_it 6.273 r_scbond_other 6.269 r_dihedral_angle_2_deg 3.568 r_rigid_bond_restr 2.978 r_angle_refined_deg 1.442 r_angle_other_deg 0.524 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1423 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction MOLREP phasing PDB_EXTRACT data extraction