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Crystal Structure of the first bromodomain of human BRD4 in complex with a quinazolin ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.2M NaNO3, 0.1M BTProp pH 6.5, 20% PEG3350, 10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.11 41.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.69 α = 90 b = 46.4 β = 90 c = 76.87 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 2011-12-17 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 1.63 32.37 96.6 0.066 0.066 12.4 3.9 16494 15933 20.8
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 1.63 1.72 85.7 0.354 0.354 2.2 2.7 1998
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 2OSS 1.63 32.37 16527 15896 802 96.18 0.2064 0.2064 0.2047 0.2093 0.2406 0.2486 RANDOM 24.7949
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] 2.98 -1.41 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.422 r_dihedral_angle_4_deg 21.944 r_dihedral_angle_3_deg 12.154 r_dihedral_angle_1_deg 6.022 r_angle_refined_deg 1.621 r_angle_other_deg 0.993 r_chiral_restr 0.091 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.422 r_dihedral_angle_4_deg 21.944 r_dihedral_angle_3_deg 12.154 r_dihedral_angle_1_deg 6.022 r_angle_refined_deg 1.621 r_angle_other_deg 0.993 r_chiral_restr 0.091 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1050 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 21
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction