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Crystal Structure of the first bromodomain of human BRD4 in complex with a isoxazolylbenzimidazole ligand
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 6.5 277 0.20M Na2SO4, 0.1M BTProp, 20.0% PEG 3350, 10.0% EtGly, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.17 43.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.29 α = 90 b = 44.38 β = 90 c = 79.12 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 2010-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
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 22.672 98.4 0.085 0.085 11.3 4.6 17955 17668 18.6
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 94.3 0.298 0.298 2.5 4.1 2411
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 22.672 17962 17632 905 98.16 0.1672 0.1672 0.1652 0.1733 0.2042 0.2076 RANDOM 17.7235
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] 0.8 -0.39 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.511 r_dihedral_angle_4_deg 12.905 r_dihedral_angle_3_deg 11.356 r_scangle_it 6.944 r_dihedral_angle_1_deg 5.591 r_scbond_it 5.264 r_mcangle_it 3.491 r_mcbond_it 2.218 r_angle_refined_deg 1.627 r_angle_other_deg 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.511 r_dihedral_angle_4_deg 12.905 r_dihedral_angle_3_deg 11.356 r_scangle_it 6.944 r_dihedral_angle_1_deg 5.591 r_scbond_it 5.264 r_mcangle_it 3.491 r_mcbond_it 2.218 r_angle_refined_deg 1.627 r_angle_other_deg 0.99 r_mcbond_other 0.681 r_chiral_restr 0.099 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1050 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 32
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction