☰ Navigation Tabs
Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H3K9ac/K14ac)
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 7.5 277 0.20M Na(acetate)
0.1M BTProp pH 7.5
20.0% PEG 3350
10.0% EtGly
Crystal Properties Matthews coefficient Solvent content 2.02 39.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.63 α = 90 b = 50.49 β = 89.99 c = 64.54 γ = 90
Symmetry Space Group P 1 21 1
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 2012-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 1.61 19.82 99.2 0.081 0.081 0.041 0.041 9.9 4.9 18357
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 2.2 2.32 98.2 0.635 0.635 2.2 3 1952
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 1.82 19.82 18357 1173 92.92 0.21015 0.20604 0.2136 0.28495 0.284 RANDOM 24.332
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 0.08 1.03 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.748 r_dihedral_angle_3_deg 15.904 r_dihedral_angle_4_deg 15.038 r_scangle_other 9.548 r_long_range_B_other 9.072 r_long_range_B_refined 9.065 r_scbond_it 8.262 r_scbond_other 8.259 r_dihedral_angle_1_deg 6.882 r_mcangle_other 6.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.748 r_dihedral_angle_3_deg 15.904 r_dihedral_angle_4_deg 15.038 r_scangle_other 9.548 r_long_range_B_other 9.072 r_long_range_B_refined 9.065 r_scbond_it 8.262 r_scbond_other 8.259 r_dihedral_angle_1_deg 6.882 r_mcangle_other 6.136 r_mcangle_it 6.131 r_mcbond_it 5.708 r_mcbond_other 5.696 r_angle_refined_deg 2.307 r_angle_other_deg 1.22 r_chiral_restr 0.15 r_bond_refined_d 0.026 r_gen_planes_refined 0.016 r_bond_other_d 0.002 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 2188 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 4
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement Coot model building