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Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor TG-101348
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OSS PDB ENTRY 2OSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.20 M sodium potassium tartrate, 0.1 M Bis-Tris propane, pH 7.5, 20.0% PEG3350, 10% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.32 46.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.163 α = 90 b = 59.412 β = 90 c = 111.67 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 IMAGE PLATE RIGAKU RAXIS IV 2013-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.52
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.65 19.561 99.3 0.051 0.051 17.9 4.5 34602 34360 16.2
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 1.65 1.74 96.5 0.271 0.271 2.9 3.7 4769
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 2OSS 1.65 19.56 34568 34298 1726 99.22 0.1519 0.1519 0.1503 0.1633 0.1817 0.1908 RANDOM 18.795
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] 0.41 0.04 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.303 r_dihedral_angle_4_deg 18.519 r_dihedral_angle_3_deg 12.714 r_dihedral_angle_1_deg 5.117 r_mcangle_it 3.837 r_mcbond_it 3.584 r_mcbond_other 3.342 r_angle_refined_deg 1.765 r_angle_other_deg 1.145 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.303 r_dihedral_angle_4_deg 18.519 r_dihedral_angle_3_deg 12.714 r_dihedral_angle_1_deg 5.117 r_mcangle_it 3.837 r_mcbond_it 3.584 r_mcbond_other 3.342 r_angle_refined_deg 1.765 r_angle_other_deg 1.145 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2112 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 86
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection XDS data reduction