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Crystal Structure of the first bromodomain of human BRD4 in complex with an acetylated BAZ1B peptide (K221ac)
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, SITTING DROP 8.5 277 20% PEG3350
10% ethylene glycol
0.1M bis-tris-propane pH 8.5
0.02M sodium/potassium phosphate
Crystal Properties Matthews coefficient Solvent content 2 38.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.439 α = 90 b = 43.915 β = 90 c = 79.69 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 2016-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.15 29.51 99.1 0.037 0.037 0.015 0.015 33.9 6.8 47482
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.15 1.21 99.3 0.084 0.084 15.5 5.8 6775
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 1.15 29.51 45469 1946 99.85 0.12002 0.11893 0.1188 0.14448 0.1428 RANDOM 12.17
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] 0.78 -0.33 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.026 r_sphericity_free 19.017 r_dihedral_angle_4_deg 13.75 r_dihedral_angle_3_deg 12.823 r_sphericity_bonded 6.513 r_dihedral_angle_1_deg 5.846 r_long_range_B_refined 2.501 r_long_range_B_other 2.187 r_scangle_other 2.117 r_rigid_bond_restr 1.924
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.026 r_sphericity_free 19.017 r_dihedral_angle_4_deg 13.75 r_dihedral_angle_3_deg 12.823 r_sphericity_bonded 6.513 r_dihedral_angle_1_deg 5.846 r_long_range_B_refined 2.501 r_long_range_B_other 2.187 r_scangle_other 2.117 r_rigid_bond_restr 1.924 r_scbond_other 1.722 r_scbond_it 1.721 r_angle_refined_deg 1.715 r_mcangle_other 1.479 r_mcangle_it 1.476 r_mcbond_it 1.155 r_mcbond_other 1.144 r_angle_other_deg 1.088 r_chiral_restr 0.112 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.002 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1119 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing Coot model building