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Crystal structure of the first bromodomain of human BRD4 with benzotriazolo-diazepine scaffold
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Internal model of BRD4-BD1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2 M potassium sodium tartrate and 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.18 43.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.376 α = 82.6 b = 39.508 β = 75.43 c = 57.358 γ = 90
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 MX-300 2015-01-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9795 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.06 50 91.4 0.055 14.6 2.1 105981
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.06 1.1 77.9 0.34 2.2 1.7 9046
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 of BRD4-BD1 1.06 50 100690 5291 91.27 0.1871 0.1854 0.1925 0.2196 0.2273 RANDOM 14.553
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] 0.52 -0.28 -0.89 -1.26 0.46 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.333 r_sphericity_free 21.485 r_dihedral_angle_4_deg 17.177 r_dihedral_angle_3_deg 13.755 r_sphericity_bonded 8.203 r_rigid_bond_restr 6.924 r_dihedral_angle_1_deg 5.486 r_angle_refined_deg 2.347 r_mcangle_it 1.628 r_mcbond_it 1.391
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.333 r_sphericity_free 21.485 r_dihedral_angle_4_deg 17.177 r_dihedral_angle_3_deg 13.755 r_sphericity_bonded 8.203 r_rigid_bond_restr 6.924 r_dihedral_angle_1_deg 5.486 r_angle_refined_deg 2.347 r_mcangle_it 1.628 r_mcbond_it 1.391 r_mcbond_other 1.378 r_angle_other_deg 1.068 r_chiral_restr 0.141 r_bond_refined_d 0.028 r_gen_planes_refined 0.014 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2085 Nucleic Acid Atoms Solvent Atoms 308 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing