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N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH (S)-5-(1-((1-(1-isopropylpiperidine-4-carbonyl)piperidin-3-yl)methyl)-1H-benzo[d]imidazol-2-yl)-1,3-dimethylpyridin-2(1H)-one
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other in house structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 0.1M Tris pH8.5, 12% w/v PEG4K
Crystal Properties Matthews coefficient Solvent content 2.07 40.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.845 α = 90 b = 47.236 β = 90 c = 58.974 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 2019-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979507 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.3 58.97 98.5 0.06 0.999 13.8 5.8 31016
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.37 90.4 0.475 0.751 1.9 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.3 32.544 30959 1588 98.304 0.199 0.1984 0.2078 0.2175 0.2264 17.014
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] -0.18 0.009 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.453 r_dihedral_angle_3_deg 10.913 r_dihedral_angle_4_deg 8.102 r_dihedral_angle_1_deg 5.887 r_lrange_it 4.634 r_lrange_other 4.174 r_scangle_it 2.058 r_scangle_other 2.057 r_mcangle_it 1.398 r_mcangle_other 1.393
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.453 r_dihedral_angle_3_deg 10.913 r_dihedral_angle_4_deg 8.102 r_dihedral_angle_1_deg 5.887 r_lrange_it 4.634 r_lrange_other 4.174 r_scangle_it 2.058 r_scangle_other 2.057 r_mcangle_it 1.398 r_mcangle_other 1.393 r_scbond_it 1.276 r_scbond_other 1.275 r_angle_other_deg 1.203 r_angle_refined_deg 1.193 r_mcbond_it 0.855 r_mcbond_other 0.849 r_nbd_refined 0.189 r_nbtor_refined 0.172 r_symmetry_nbd_other 0.165 r_nbd_other 0.152 r_xyhbond_nbd_refined 0.128 r_symmetry_xyhbond_nbd_refined 0.12 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.062 r_symmetry_nbd_refined 0.058 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1046 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling