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Crystal structure of the first bromodomain of human BRD4 in complex with the inhibitor 16i
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 6.5 293 30% pentaerythritol ethoxylate 15/4, 0.05 ammonium sulfate, 0.1M bis-tris pH6.5
Crystal Properties Matthews coefficient Solvent content 2.14 42.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.34 α = 83.93 b = 39.53 β = 75.64 c = 56.03 γ = 89.75
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 2M 2018-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.918400 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.2 39.3 83 0.055 9.6 3.7 65153
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 76.9 0.886
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 39.3 63278 1874 83.02 0.14318 0.14174 0.1457 0.17595 0.1833 RANDOM 15.016
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] -0.3 0.19 -0.38 -0.89 -0.17 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.946 r_dihedral_angle_4_deg 13.808 r_dihedral_angle_3_deg 11.153 r_dihedral_angle_1_deg 5.803 r_long_range_B_other 3.248 r_long_range_B_refined 3.247 r_rigid_bond_restr 3.241 r_scangle_other 3.164 r_scbond_it 2.788 r_scbond_other 2.787
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.946 r_dihedral_angle_4_deg 13.808 r_dihedral_angle_3_deg 11.153 r_dihedral_angle_1_deg 5.803 r_long_range_B_other 3.248 r_long_range_B_refined 3.247 r_rigid_bond_restr 3.241 r_scangle_other 3.164 r_scbond_it 2.788 r_scbond_other 2.787 r_mcangle_other 1.911 r_mcangle_it 1.887 r_mcbond_it 1.624 r_mcbond_other 1.573 r_angle_refined_deg 1.499 r_angle_other_deg 1.425 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2070 Nucleic Acid Atoms Solvent Atoms 329 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing