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C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH (S)-5-(1-((1-acetylpiperidin-3-yl)methyl)-5-bromo-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
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 30% PEG 300, 0.1M MES buffer pH6.5
Crystal Properties Matthews coefficient Solvent content 2.25 45.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.825 α = 90 b = 52.573 β = 90 c = 31.975 γ = 90
Symmetry Space Group P 21 21 2
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 RIGAKU SATURN A200 2014-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178
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 1.6 71.82 96.6 0.018 40.9 3.3 15930
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 81 0.068 12.2 2
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 FOURIER SYNTHESIS FREE R-VALUE 1.603 42.423 15868 766 96.141 0.145 0.1436 0.1565 0.1713 0.1858 14.874
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] 0.818 -0.794 -0.024
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.099 r_dihedral_angle_3_deg 13.176 r_lrange_it 6.491 r_lrange_other 6.489 r_dihedral_angle_1_deg 5.092 r_dihedral_angle_2_deg 4.629 r_scangle_it 3.091 r_scangle_other 3.089 r_scbond_it 1.918 r_scbond_other 1.916
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.099 r_dihedral_angle_3_deg 13.176 r_lrange_it 6.491 r_lrange_other 6.489 r_dihedral_angle_1_deg 5.092 r_dihedral_angle_2_deg 4.629 r_scangle_it 3.091 r_scangle_other 3.089 r_scbond_it 1.918 r_scbond_other 1.916 r_mcangle_other 1.501 r_mcangle_it 1.497 r_angle_refined_deg 1.085 r_mcbond_it 0.951 r_mcbond_other 0.904 r_angle_other_deg 0.411 r_nbd_refined 0.23 r_nbtor_refined 0.189 r_symmetry_nbd_other 0.173 r_symmetry_nbd_refined 0.138 r_xyhbond_nbd_refined 0.133 r_nbd_other 0.131 r_symmetry_xyhbond_nbd_refined 0.129 r_symmetry_nbtor_other 0.069 r_chiral_restr 0.061 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 910 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling