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Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor PFi-1
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 8.5 277 0.2M Na(malonate)
0.1M BTProp pH 8.5
20% PEG3350
10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.1 41.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.71 α = 90 b = 46.71 β = 90 c = 78.25 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 2011-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54178
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 1.91 23.355 99.5 0.11 0.11 8.8 4.6 10464 10412 26.5
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 1.91 2.01 99 0.819 0.819 0.9 4.6 1479
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 1.92 23.35 10208 10125 489 99.19 0.2159 0.2159 0.2126 0.2135 0.2855 0.2876 RANDOM 28.7881
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] 4 -2.1 -1.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.106 r_dihedral_angle_3_deg 15.524 r_dihedral_angle_4_deg 15.075 r_scangle_it 9.941 r_scbond_it 8.435 r_dihedral_angle_1_deg 5.849 r_mcangle_it 5.556 r_mcbond_it 4.251 r_angle_refined_deg 1.512 r_mcbond_other 1.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.106 r_dihedral_angle_3_deg 15.524 r_dihedral_angle_4_deg 15.075 r_scangle_it 9.941 r_scbond_it 8.435 r_dihedral_angle_1_deg 5.849 r_mcangle_it 5.556 r_mcbond_it 4.251 r_angle_refined_deg 1.512 r_mcbond_other 1.421 r_angle_other_deg 0.991 r_chiral_restr 0.079 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1020 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 33
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction