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Crystal structure of the Bromo domain 1 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 7.5 277 0.2M NaNO3, 20% PEG3350, 10% Ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.14 42.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.418 α = 90 b = 44.139 β = 90 c = 78.413 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 CCD MARMOSAIC 225 mm CCD 2007-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97910 SLS X10SA
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 1.35 50 99.9 0.071 0.071 14.1 8.1 29349 29320
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 1.35 1.4 100 0.177 6.5 2874
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 1.35 39.19 29280 29262 1485 99.94 0.15 0.15 0.149 0.1483 0.174 0.1736 RANDOM 8.628
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] 0.16 -0.02 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.633 r_dihedral_angle_3_deg 10.633 r_dihedral_angle_4_deg 8.232 r_dihedral_angle_1_deg 5.497 r_sphericity_free 3.78 r_scangle_it 2.903 r_scbond_it 2.091 r_sphericity_bonded 2.046 r_mcangle_it 1.528 r_angle_refined_deg 1.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.633 r_dihedral_angle_3_deg 10.633 r_dihedral_angle_4_deg 8.232 r_dihedral_angle_1_deg 5.497 r_sphericity_free 3.78 r_scangle_it 2.903 r_scbond_it 2.091 r_sphericity_bonded 2.046 r_mcangle_it 1.528 r_angle_refined_deg 1.298 r_rigid_bond_restr 1.144 r_mcbond_it 1.112 r_angle_other_deg 0.909 r_mcbond_other 0.354 r_symmetry_vdw_refined 0.291 r_symmetry_vdw_other 0.278 r_nbd_refined 0.219 r_nbtor_refined 0.189 r_nbd_other 0.171 r_xyhbond_nbd_refined 0.134 r_symmetry_hbond_refined 0.094 r_nbtor_other 0.09 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1047 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 12
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction