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C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1,3-dimethyl-5-(1-((tetrahydro-2H-pyran-4-yl)methyl)-1H-benzo[d]imidazol-2-yl)pyridin-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 6.5 293 30% PEG 300, 0.1M MES buffer pH6.5
Crystal Properties Matthews coefficient Solvent content 2.27 45.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.949 α = 90 b = 52.631 β = 90 c = 32.159 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 2014-09-12 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 1.62 71.95 96.7 0.024 26.6 2.7 15520
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 1.62 1.71 83.6 0.17 5.6 1.9
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 FOURIER SYNTHESIS FREE R-VALUE 1.622 27.442 15429 765 95.922 0.153 0.1517 0.1563 0.1769 0.1796 15.117
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] 0.053 -0.002 -0.051
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.908 r_dihedral_angle_3_deg 13.468 r_lrange_it 6.7 r_lrange_other 6.7 r_dihedral_angle_1_deg 4.972 r_dihedral_angle_2_deg 3.47 r_scangle_it 2.809 r_scangle_other 2.807 r_scbond_other 1.71 r_scbond_it 1.708
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.908 r_dihedral_angle_3_deg 13.468 r_lrange_it 6.7 r_lrange_other 6.7 r_dihedral_angle_1_deg 4.972 r_dihedral_angle_2_deg 3.47 r_scangle_it 2.809 r_scangle_other 2.807 r_scbond_other 1.71 r_scbond_it 1.708 r_mcangle_it 1.653 r_mcangle_other 1.653 r_angle_refined_deg 1.044 r_mcbond_it 1.012 r_mcbond_other 0.978 r_angle_other_deg 0.4 r_nbd_refined 0.22 r_symmetry_nbd_refined 0.216 r_nbtor_refined 0.187 r_symmetry_nbd_other 0.176 r_nbd_other 0.155 r_xyhbond_nbd_refined 0.145 r_symmetry_xyhbond_nbd_refined 0.099 r_symmetry_nbtor_other 0.07 r_chiral_restr 0.06 r_gen_planes_refined 0.005 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 931 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling