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Crystal Structure of the first bromodomain of BRD4 in complex with RT53
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 20% PEG3350
10% ethylene glycol
0.1M bis-tris-propane pH 8.5
0.02M sodium/potassium phosphate
Crystal Properties Matthews coefficient Solvent content 2.22 44.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.671 α = 90 b = 44.795 β = 90 c = 79.549 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 DECTRIS PILATUS 6M 2017-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.2 29.74 99.9 0.038 0.038 0.042 0.017 32.9 5.8 42878
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.26 99.3 0.054 0.054 0.062 0.029 13 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2OSS 1.2 29.74 41667 1146 99.79 0.1193 0.1188 0.1185 0.1365 0.1378 RANDOM 10.47
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] 0.39 -0.29 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.41 r_sphericity_free 16.636 r_dihedral_angle_3_deg 10.761 r_dihedral_angle_4_deg 9.046 r_sphericity_bonded 6.975 r_dihedral_angle_1_deg 5.524 r_angle_refined_deg 1.744 r_angle_other_deg 1.614 r_rigid_bond_restr 1.022 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.41 r_sphericity_free 16.636 r_dihedral_angle_3_deg 10.761 r_dihedral_angle_4_deg 9.046 r_sphericity_bonded 6.975 r_dihedral_angle_1_deg 5.524 r_angle_refined_deg 1.744 r_angle_other_deg 1.614 r_rigid_bond_restr 1.022 r_chiral_restr 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1044 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing