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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 8 277 20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly, pH 8.0
Crystal Properties Matthews coefficient Solvent content 1.94 36.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.92 α = 90 b = 47.34 β = 90 c = 78.37 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 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 2.12 78.37 94.1 0.097 0.039 0.993 10.8 7.4 7346
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 2.12 2.18 99.7 0.251 0.094 0.985 5.7 8.1 640
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 2.12 40.52 6935 375 93.6 0.2274 0.2258 0.2319 0.2567 0.2513 RANDOM 32.145
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] 6.55 -2.82 -3.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.983 r_dihedral_angle_3_deg 12.855 r_dihedral_angle_4_deg 10.809 r_dihedral_angle_1_deg 5.243 r_mcangle_it 1.306 r_angle_refined_deg 1.108 r_angle_other_deg 0.883 r_mcbond_other 0.726 r_mcbond_it 0.725 r_chiral_restr 0.054
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.983 r_dihedral_angle_3_deg 12.855 r_dihedral_angle_4_deg 10.809 r_dihedral_angle_1_deg 5.243 r_mcangle_it 1.306 r_angle_refined_deg 1.108 r_angle_other_deg 0.883 r_mcbond_other 0.726 r_mcbond_it 0.725 r_chiral_restr 0.054 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1115 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction MOSFLM data reduction MOLREP phasing