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Crystal structure of TRIM24 PHD-bromodomain complexed with N-(1,3-dimethyl-2-oxo-2,3-dihydro-1H-1,3-benzodiazol-5-yl)-4-methoxybenzene-1-sulfonamide (5b)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O34
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 2.2-2.4M ammonium sulfate, 0.1M HEPES buffer pH 7.5, 2% PEG400 and 8-9% glycerol
Crystal Properties Matthews coefficient Solvent content 2.42 49.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.99 α = 107.78 b = 49.236 β = 90 c = 65.77 γ = 112.06
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2013-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1159 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.18 62.1 91.9 0.111 3.7 2.1 21176
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.18 2.25 92.8 0.373 2.2 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3O34 2.18 62.1 20798 1090 98.2 0.115 0.112 0.1248 0.165 0.1674 RANDOM 34.58
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] 0.25 0.12 0.06 0.28 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.255 r_dihedral_angle_3_deg 15.069 r_dihedral_angle_4_deg 8.218 r_dihedral_angle_1_deg 6.459 r_mcangle_it 3.735 r_mcbond_it 2.593 r_mcbond_other 2.581 r_angle_refined_deg 1.702 r_angle_other_deg 0.903 r_chiral_restr 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.255 r_dihedral_angle_3_deg 15.069 r_dihedral_angle_4_deg 8.218 r_dihedral_angle_1_deg 6.459 r_mcangle_it 3.735 r_mcbond_it 2.593 r_mcbond_other 2.581 r_angle_refined_deg 1.702 r_angle_other_deg 0.903 r_chiral_restr 0.108 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2806 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction MOSFLM data reduction