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Crystal Structure of the first bromodomain of BRD4 in complex with B16
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IOO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 0.20M Sodium Nitrate, 20% PEG 3350, 10% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.15 42.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.411 α = 90 b = 44.392 β = 90 c = 78.246 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 PIXEL PSI PILATUS 6M 2014-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.99989 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.25 44.392 98.7 0.084 0.088 0.026 16.3 11.7 36350 36350
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.32 91.7 0.617 0.617 0.231 1.1 8.2 4815
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4ioo 1.25 39.123 1.33 36281 1799 98.5 0.1467 0.1456 0.1468 0.1687 0.1681
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.745 f_angle_d 1.175 f_chiral_restr 0.058 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1015 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 39
Software Software Software Name Purpose PHENIX refinement SCALA data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction