☰ Navigation Tabs
Crystal Structure of the first bromodomain of human BRD4 in complex with benzo[cd]indol-2(1H)-one ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MXF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 277 20% PEG3350, 0.2M NaCl, 0.1M HEPES, 10% EtGhly,pH 7.8
Crystal Properties Matthews coefficient Solvent content 2.57 52.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.05 α = 90 b = 54.05 β = 90 c = 50.69 γ = 120
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 PSI PILATUS 6M 2015-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON OTHER 0.97852
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.55 46.81 90.5 0.064 0.023 0.999 14.7 7.8 21754
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 95.2 0.356 0.155 0.934 3.2 5.9 1109
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 3MXF 1.55 46.81 20541 1192 90.52 0.16501 0.16317 0.1751 0.19788 0.2087 RANDOM 19.902
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] -0.33 -0.17 -0.33 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.061 r_dihedral_angle_4_deg 17.072 r_dihedral_angle_3_deg 11.307 r_long_range_B_refined 5.075 r_long_range_B_other 5.073 r_dihedral_angle_1_deg 5.012 r_scangle_other 3.355 r_scbond_it 2.072 r_scbond_other 2.072 r_mcangle_it 1.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.061 r_dihedral_angle_4_deg 17.072 r_dihedral_angle_3_deg 11.307 r_long_range_B_refined 5.075 r_long_range_B_other 5.073 r_dihedral_angle_1_deg 5.012 r_scangle_other 3.355 r_scbond_it 2.072 r_scbond_other 2.072 r_mcangle_it 1.939 r_mcangle_other 1.937 r_angle_refined_deg 1.512 r_mcbond_it 1.213 r_mcbond_other 1.213 r_angle_other_deg 1.087 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.004 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 1091 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction MOSFLM data reduction MOLREP phasing