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Crystal Structure of the first bromodomain of human BRD4 in complex with a quinazoline 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 8.5 277 0.20M K3(cit), 0.1M BTProp pH 8.5, 20.0% PEG 3350, 10.0% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.16 43.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.65 α = 90 b = 46.02 β = 90 c = 77.31 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 2010-11-03 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 1.685 29.6 100 0.097 0.097 9.1 4.5 15402 15402 22.2
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 1.68 1.78 100 0.592 0.592 1.3 4.3 2189
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 1.69 29.6 15359 15356 767 99.98 0.1769 0.1769 0.1744 0.1765 0.2283 0.231 RANDOM 20.7642
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] 1.61 -0.71 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.999 r_dihedral_angle_4_deg 29.497 r_dihedral_angle_3_deg 13.805 r_scangle_it 7.243 r_scbond_it 6.206 r_dihedral_angle_1_deg 5.168 r_mcangle_it 3.919 r_mcbond_it 2.572 r_angle_refined_deg 1.575 r_angle_other_deg 0.947
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.999 r_dihedral_angle_4_deg 29.497 r_dihedral_angle_3_deg 13.805 r_scangle_it 7.243 r_scbond_it 6.206 r_dihedral_angle_1_deg 5.168 r_mcangle_it 3.919 r_mcbond_it 2.572 r_angle_refined_deg 1.575 r_angle_other_deg 0.947 r_mcbond_other 0.909 r_chiral_restr 0.333 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 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 170 Heterogen Atoms 23
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction