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Human TRIM21 PRYSPRY domain in complex with compound 28 (Z38)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 12% PEG 20.000
0.1 M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.08 40.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.264 α = 90 b = 52.064 β = 90 c = 70.904 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 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 1.3 52.06 96.2 0.035 0.036 0.01 1 43.9 12.5 41179
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 1.3 1.32 70.2 0.114 0.123 0.043 0.991 7.7
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 1.3 41.97 39045 2079 95.96 0.13529 0.1342 0.1443 0.15577 0.1613 RANDOM 8.526
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] -0.14 -0.24 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.568 r_long_range_B_refined 8.702 r_long_range_B_other 8.7 r_dihedral_angle_1_deg 7.211 r_dihedral_angle_2_deg 5.038 r_scangle_other 3.034 r_mcangle_other 2.476 r_mcangle_it 2.474 r_scbond_other 1.936 r_scbond_it 1.933
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.568 r_long_range_B_refined 8.702 r_long_range_B_other 8.7 r_dihedral_angle_1_deg 7.211 r_dihedral_angle_2_deg 5.038 r_scangle_other 3.034 r_mcangle_other 2.476 r_mcangle_it 2.474 r_scbond_other 1.936 r_scbond_it 1.933 r_rigid_bond_restr 1.77 r_mcbond_it 1.504 r_mcbond_other 1.495 r_angle_refined_deg 1.389 r_angle_other_deg 0.491 r_chiral_restr 0.071 r_gen_planes_refined 0.007 r_bond_refined_d 0.004 r_gen_planes_other 0.003 r_bond_other_d 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 1443 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction MOLREP phasing PDB_EXTRACT data extraction