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FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR 4-[(1-methyl-2-oxo-1,2-dihydroquinolin-4-yl)oxy]-N-({1-[(3-methylphe methyl]piperidin-4-yl}methyl)butanamide
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 NaNO3. 5.0 mM inhibitor (in DMSO) final concentration. Cryoprotection with 10% (w/v) glycerol.
Crystal Properties Matthews coefficient Solvent content 2.15 42.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.263 α = 90 b = 44.236 β = 90 c = 78.436 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 2006-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87260 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 1.7 50 96.3 0.149 7.54 4.47 14342
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 1.7 1.8 95.2 0.421 4.15 4.38
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 1.7 39.22 13624 718 96.29 0.25529 0.25122 0.2587 0.3339 0.3342 RANDOM 12.795
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] 2.46 -1.01 -1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.371 r_dihedral_angle_4_deg 24.098 r_sphericity_free 19.76 r_dihedral_angle_3_deg 14.115 r_sphericity_bonded 8.873 r_dihedral_angle_1_deg 7.868 r_long_range_B_refined 3.128 r_long_range_B_other 3.096 r_scangle_other 3.087 r_scbond_it 2.576
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.371 r_dihedral_angle_4_deg 24.098 r_sphericity_free 19.76 r_dihedral_angle_3_deg 14.115 r_sphericity_bonded 8.873 r_dihedral_angle_1_deg 7.868 r_long_range_B_refined 3.128 r_long_range_B_other 3.096 r_scangle_other 3.087 r_scbond_it 2.576 r_scbond_other 2.574 r_rigid_bond_restr 2.423 r_angle_refined_deg 2.329 r_mcangle_it 2.251 r_mcangle_other 2.251 r_mcbond_it 1.957 r_mcbond_other 1.949 r_angle_other_deg 1.473 r_chiral_restr 0.135 r_bond_refined_d 0.028 r_gen_planes_refined 0.012 r_bond_other_d 0.007 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 1062 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 34
Software Software Software Name Purpose XDS data reduction XDS data scaling PHASER phasing REFMAC refinement