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Human TRIM21 PRYSPRY domain in complex with compound 29 (Z37)
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 8.2 293 0.056 M Sodium Phosphate Monobasic
1.344 M Potassium Phosphate Dibasic
Crystal Properties Matthews coefficient Solvent content 2.79 55.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.542 α = 90 b = 97.542 β = 90 c = 48.174 γ = 90
Symmetry Space Group P 41 21 2
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 2025-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.95373 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 1.8 48.82 100 0.089 0.09 0.018 1 21.1 26.6 22156
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 1.8 1.84 100 2.753 2.805 0.532 0.798 27.7
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 1.8 48.82 20990 1092 99.88 0.1942 0.19258 0.2062 0.22389 0.2339 RANDOM 38.833
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] -2.73 -2.73 5.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.115 r_dihedral_angle_1_deg 7.787 r_long_range_B_other 7.311 r_long_range_B_refined 7.305 r_scangle_other 5.498 r_dihedral_angle_2_deg 4.688 r_mcangle_it 4.64 r_mcangle_other 4.638 r_scbond_it 3.712 r_scbond_other 3.709
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.115 r_dihedral_angle_1_deg 7.787 r_long_range_B_other 7.311 r_long_range_B_refined 7.305 r_scangle_other 5.498 r_dihedral_angle_2_deg 4.688 r_mcangle_it 4.64 r_mcangle_other 4.638 r_scbond_it 3.712 r_scbond_other 3.709 r_mcbond_it 3.114 r_mcbond_other 3.114 r_angle_refined_deg 1.477 r_angle_other_deg 0.511 r_chiral_restr 0.068 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1429 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction MOLREP phasing PDB_EXTRACT data extraction