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FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR N-{3-[4-(3-chlorophenyl)piperazin-1-yl]propyl}-1-{3-methyl-[1,2,4]triazolo[4,3-b]pyridazin-6-yl}piperidine-4-carboxamide
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 7.5 292 Ratio 1:1 (protein:precipitant). 12 mg/mL Brd4_BD1 protein. Protein buffer 10 mM HEPES (pH 7.5) 150 mM NaCl. Precipitant agent 22 % (w/v) PEG 3350, 10% (w/v) ethylene glycol 30 % (w/v), 0.3 M NaFormate. 1.0 mM inhibitor (in DMSO) final concentration. Cryoprotection with 10 % (w/v) glycerol
Crystal Properties Matthews coefficient Solvent content 1.96 37.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.723 α = 90 b = 48.509 β = 90 c = 58.094 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 2M 2015-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.967700 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.9 50 99.3 0.042 20.09 4.83 9664
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2.02 97.8 0.379 3.73 4.59
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 1.9 37.23 9180 484 99.31 0.12959 0.12547 0.1388 0.20707 0.2154 RANDOM 42.711
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] -0.31 2.31 -1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.356 r_sphericity_free 33.033 r_sphericity_bonded 27.128 r_dihedral_angle_4_deg 16.734 r_dihedral_angle_3_deg 15.091 r_scangle_other 12.271 r_long_range_B_other 11.421 r_long_range_B_refined 11.394 r_scbond_it 10.885 r_scbond_other 10.877
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.356 r_sphericity_free 33.033 r_sphericity_bonded 27.128 r_dihedral_angle_4_deg 16.734 r_dihedral_angle_3_deg 15.091 r_scangle_other 12.271 r_long_range_B_other 11.421 r_long_range_B_refined 11.394 r_scbond_it 10.885 r_scbond_other 10.877 r_mcangle_other 9.367 r_mcangle_it 9.197 r_mcbond_it 8.314 r_mcbond_other 7.891 r_dihedral_angle_1_deg 5.498 r_rigid_bond_restr 5.035 r_angle_refined_deg 2.316 r_angle_other_deg 1.251 r_chiral_restr 0.121 r_bond_refined_d 0.028 r_gen_planes_refined 0.011 r_bond_other_d 0.005 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1043 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 35
Software Software Software Name Purpose XDS data reduction XDS data scaling PHASER phasing REFMAC refinement