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First domain of human bromodomain BRD4 in complex with inhibitor 8-(5-Amino-1H-[1,2,4]triazol-3-ylsulfanylmethyl)-3-(4-chlorobenzyl)-7-ethyl-3,7-dihydropurine-2,6-dione
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 292 Ratio 1:1 (protein:precipitant). 12 mg/mL BRD4_BD1 protein. 2.5 mM inhibitor (in DMSO) final concentration. Protein buffer: 0.01M HEPES (pH 7.5), 0.15M NaCl. Precipitant agent : 0.3M Na Formate, 0.1M NaCl, 22% PEG3350, 10% ethylene glycol. Cryoprotectant : 10% ethylene glycol.
Crystal Properties Matthews coefficient Solvent content 2.14 42.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.353 α = 90 b = 44.069 β = 90 c = 78.272 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 PILATUS 6M-F 2009-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.972390 ESRF ID29
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 1.05 50 99.5 0.074 11.16 5.05 60686
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 1.05 1.11 98.6 0.481 0.432 4.65
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 2OSS 1.05 39.14 57651 3035 99.53 0.17186 0.17082 0.1797 0.19195 0.2009 RANDOM 11.245
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] 0.57 -0.3 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.464 r_dihedral_angle_4_deg 19.798 r_dihedral_angle_3_deg 12.129 r_dihedral_angle_1_deg 6.249 r_long_range_B_refined 5.506 r_long_range_B_other 5.504 r_scangle_other 3.467 r_scbond_it 2.418 r_angle_refined_deg 2.417 r_scbond_other 2.416
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.464 r_dihedral_angle_4_deg 19.798 r_dihedral_angle_3_deg 12.129 r_dihedral_angle_1_deg 6.249 r_long_range_B_refined 5.506 r_long_range_B_other 5.504 r_scangle_other 3.467 r_scbond_it 2.418 r_angle_refined_deg 2.417 r_scbond_other 2.416 r_mcangle_other 1.816 r_mcangle_it 1.813 r_mcbond_it 1.36 r_mcbond_other 1.352 r_angle_other_deg 1.299 r_chiral_restr 0.153 r_bond_refined_d 0.03 r_gen_planes_refined 0.014 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 1062 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 33
Software Software Software Name Purpose XDS data reduction PHASER phasing REFMAC refinement XDS data scaling