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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 7.5 277 20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly,pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.95 36.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.03 α = 90 b = 46.27 β = 96.74 c = 47.44 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 CCD ADSC QUANTUM 315 2014-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97915 SSRF BL17U
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 1.49 47.11 90.8 0.06 0.026 0.996 23.9 7 19102
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 1.49 1.52 96.5 0.1 0.041 0.993 15.2 6.9 986
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 1.49 47.11 18213 874 90.69 0.1654 0.1645 0.1743 0.1833 0.1918 RANDOM 15.264
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] -0.32 -0.26 0.47 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.395 r_dihedral_angle_3_deg 12.899 r_dihedral_angle_4_deg 9.624 r_dihedral_angle_1_deg 5.043 r_mcangle_it 1.683 r_angle_refined_deg 1.583 r_angle_other_deg 1.054 r_mcbond_it 1.029 r_mcbond_other 1.028 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.395 r_dihedral_angle_3_deg 12.899 r_dihedral_angle_4_deg 9.624 r_dihedral_angle_1_deg 5.043 r_mcangle_it 1.683 r_angle_refined_deg 1.583 r_angle_other_deg 1.054 r_mcbond_it 1.029 r_mcbond_other 1.028 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1072 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 55
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction MOLREP phasing