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Crystal Structure of the Bromo domain 2 in human Bromodomain Containing Protein 4 (BRD4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X0J PDB entry 1X0J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 0.1M MIB, 30% PEG 1000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.37 48.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.032 α = 90 b = 73.698 β = 90 c = 33.467 γ = 90
Symmetry Space Group P 21 21 2
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 2007-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54000
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 1.74 73.72 99.3 0.065 0.065 11.4 3.7 15125 15125
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.78 98.6 0.618 3.3 1156
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 1X0J 1.89 50 12030 12030 722 98.16 0.184 0.184 0.182 0.1802 0.216 0.2129 RANDOM 27.303
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] -0.26 0.18 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.577 r_dihedral_angle_4_deg 26.097 r_dihedral_angle_3_deg 11.279 r_dihedral_angle_1_deg 5.308 r_scangle_it 2.936 r_scbond_it 2.144 r_angle_refined_deg 1.531 r_mcangle_it 1.455 r_mcbond_it 1.053 r_angle_other_deg 1.048
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.577 r_dihedral_angle_4_deg 26.097 r_dihedral_angle_3_deg 11.279 r_dihedral_angle_1_deg 5.308 r_scangle_it 2.936 r_scbond_it 2.144 r_angle_refined_deg 1.531 r_mcangle_it 1.455 r_mcbond_it 1.053 r_angle_other_deg 1.048 r_mcbond_other 0.316 r_symmetry_vdw_other 0.292 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.215 r_nbd_other 0.183 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.153 r_symmetry_hbond_refined 0.139 r_chiral_restr 0.09 r_nbtor_other 0.089 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 882 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 12
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection HKL-2000 data reduction