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Crystal structure of TRIM24 PHD-BRD in complex with N-(2-(2-(2-acetamidoethoxy)ethoxy)ethyl)-3-(N-(1,3-dimethyl-2-oxo-6-(3-propoxyphenoxy)-2,3-dihydro-1H-benzo[d]imidazol-5-yl)sulfamoyl)benzamide (PEG linker unresolved)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O33
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 293 1.8 M ammonium sulfate, 0.1 M HEPES (pH 7.3), 5% PEG400
Crystal Properties Matthews coefficient Solvent content 2.37 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.942 α = 90 b = 36.652 β = 111.325 c = 65.456 γ = 90
Symmetry Space Group C 1 2 1
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 S 16M 2024-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.46 60.974 84.9 0.051 18.5 6.44 23849
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.46 1.64 0.623 2
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 1.462 60.974 23848 1232 67.98 0.153 0.1499 0.1582 0.2098 0.2122 25.956
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] 0.043 0.032 -0.159 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.534 r_lrange_it 18.876 r_lrange_other 18.804 r_scangle_it 17.478 r_scangle_other 17.471 r_dihedral_angle_6_deg 16.766 r_dihedral_angle_3_deg 15.374 r_scbond_it 12.517 r_scbond_other 12.512 r_mcangle_other 11.454
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.534 r_lrange_it 18.876 r_lrange_other 18.804 r_scangle_it 17.478 r_scangle_other 17.471 r_dihedral_angle_6_deg 16.766 r_dihedral_angle_3_deg 15.374 r_scbond_it 12.517 r_scbond_other 12.512 r_mcangle_other 11.454 r_mcangle_it 11.452 r_mcbond_it 8.242 r_mcbond_other 8.198 r_rigid_bond_restr 7.386 r_dihedral_angle_1_deg 6.404 r_angle_refined_deg 2.175 r_angle_other_deg 0.779 r_nbd_other 0.314 r_nbd_refined 0.222 r_symmetry_nbd_other 0.209 r_nbtor_refined 0.196 r_symmetry_xyhbond_nbd_refined 0.165 r_chiral_restr 0.137 r_symmetry_nbd_refined 0.137 r_xyhbond_nbd_refined 0.126 r_metal_ion_refined 0.117 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.014 r_gen_planes_other 0.013 r_gen_planes_refined 0.012 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1431 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement autoPROC data processing STARANISO data scaling PHASER phasing autoPROC data reduction