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Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor JQ1
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 NaI
0.1M BTProp pH 8.5
20% PEG3350
10% EtGhly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.14 42.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.8 α = 90 b = 44.76 β = 90 c = 78.39 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 2010-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.542
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 1.6 26.828 99.7 0.046 0.046 18.6 4.1 17716 17663 14.5
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 1.6 1.69 98.5 0.137 0.16 6.9 3.6 2467
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 1.6 26.83 17687 17609 894 99.56 0.151 0.151 0.15 0.1589 0.184 0.1976 RANDOM 14.011
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] 0.42 -0.12 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.993 r_dihedral_angle_3_deg 12.506 r_dihedral_angle_4_deg 12.292 r_scangle_it 5.323 r_dihedral_angle_1_deg 5.006 r_scbond_it 3.96 r_mcangle_it 2.802 r_mcbond_it 1.795 r_angle_refined_deg 1.698 r_angle_other_deg 0.965
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.993 r_dihedral_angle_3_deg 12.506 r_dihedral_angle_4_deg 12.292 r_scangle_it 5.323 r_dihedral_angle_1_deg 5.006 r_scbond_it 3.96 r_mcangle_it 2.802 r_mcbond_it 1.795 r_angle_refined_deg 1.698 r_angle_other_deg 0.965 r_mcbond_other 0.551 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1059 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 48
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction