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FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR 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 292 ratio 1:1 (protein:precipitant). 16 mg/mL Brd4_BD1 protein.
2.5 mM inhibitor (in DMSO) final concentration.
Protein buffer: 0.1M HEPES (pH 7.5) 0.15 mM NaCl.
Precipitant agent: 19% (w/v) PEG 3350, 0.25M ammonium sulfate,
0.1M Tris pH 8.5. Cryoprotectant: 10% (w/v) ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.15 42.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.935 α = 90 b = 46.545 β = 90 c = 77.658 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 2007-05-15 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 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 1.6 50 99.4 0.054 14.87 4.6 17766
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 1.6 1.7 98.7 0.558 2.73 4.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2OSS 1.6 39.92 16876 889 99.41 0.18448 0.18269 0.2191 0.2213 RANDOM 27.433
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] 4.27 -1.48 -2.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.202 r_dihedral_angle_4_deg 20.966 r_dihedral_angle_3_deg 14.352 r_long_range_B_other 6.379 r_long_range_B_refined 6.377 r_dihedral_angle_1_deg 6.276 r_scangle_other 4.768 r_mcangle_other 3.553 r_mcangle_it 3.537 r_scbond_it 3.413
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.202 r_dihedral_angle_4_deg 20.966 r_dihedral_angle_3_deg 14.352 r_long_range_B_other 6.379 r_long_range_B_refined 6.377 r_dihedral_angle_1_deg 6.276 r_scangle_other 4.768 r_mcangle_other 3.553 r_mcangle_it 3.537 r_scbond_it 3.413 r_scbond_other 3.413 r_mcbond_it 2.518 r_mcbond_other 2.465 r_angle_refined_deg 1.859 r_angle_other_deg 1.064 r_chiral_restr 0.107 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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 104 Heterogen Atoms 29
Software Software Software Name Purpose XDS data reduction XDS data scaling PHASER phasing REFMAC refinement