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Crystal structure of TRIM24 PHD-bromodomain with XS839112
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZQL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 Protein solution: 11 mg/ml protein in 150 mM NaCl, 25 mM HEPES, pH 7.5, 0.5 mM TCEP, 5% glycerol.
Reservoir solution: 3% PEG 400, 2.6 M ammonium sulfate, 0.1 M HEPES pH 7.5 (protein:buffer 1:2).
Crystals soaked with 0.1 mM compound in reservoir buffer complemented with 25% glycerol.
Crystal Properties Matthews coefficient Solvent content 2.34 47.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.11 α = 90 b = 36.823 β = 110.098 c = 129.419 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 XE 16M 2025-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97627 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.59 60.8 98.9 0.081 0.999 12.7 7 52968 17.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.59 1.62 98.2 0.939 0.821 2 7.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 1.59 60.8 1.33784226187 52945 2681 98.6988050631 0.150536674579 0.148110758008 0.1528 0.195692941113 0.1976 27.8269153607
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.1272286674 f_angle_d 0.807625849003 f_chiral_restr 0.0494414275424 f_bond_d 0.00595575184565 f_plane_restr 0.005126155038
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2832 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 111
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing