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Crystal structure of the first bromodomain of human BRD4 bound to benzotriazolo-diazepine scaffold
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Internal model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2 M sodium chloride, 0.1 M Bis-Tris pH 6.5, and 25% polyethylene glycol (PEG) 3350
Crystal Properties Matthews coefficient Solvent content 2.19 43.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.293 α = 83.07 b = 39.501 β = 75.35 c = 57.23 γ = 89.85
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 RAYONIX MX300HS 2015-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.399 50 84.9 0.071 0.1 0.071 10.9 1.8 42635
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.399 1.45 54.6 0.428 0.606 0.428 0.617 1.1 2749
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 Internal model 1.399 50 40551 2084 84.74 0.2053 0.2034 0.2108 0.2423 0.2427 RANDOM 16.187
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] 0.01 -0.18 0.05 -0.67 -0.22 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.981 r_dihedral_angle_4_deg 20.55 r_dihedral_angle_3_deg 15.914 r_dihedral_angle_1_deg 5.325 r_angle_refined_deg 2.064 r_mcangle_it 1.653 r_mcbond_it 1.054 r_mcbond_other 1.054 r_angle_other_deg 0.987 r_chiral_restr 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.981 r_dihedral_angle_4_deg 20.55 r_dihedral_angle_3_deg 15.914 r_dihedral_angle_1_deg 5.325 r_angle_refined_deg 2.064 r_mcangle_it 1.653 r_mcbond_it 1.054 r_mcbond_other 1.054 r_angle_other_deg 0.987 r_chiral_restr 0.125 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2091 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 60
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing