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C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1,5-dimethyl-N-(2-(methylamino)-2-oxo-1-(tetrahydro-2H-pyran-4-yl)ethyl)-6-oxo-N-(2-phenyl-2-(pyridin-2-yl)ethyl)-1,6-dihydropyridine-3-carboxamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other in house structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 30% PEG 300, 0.1M MES buffer pH6.5
Crystal Properties Matthews coefficient Solvent content 2.23 44.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.62 α = 90 b = 52.39 β = 90 c = 31.97 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 PIXEL DECTRIS EIGER X 9M 2018-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.96600 ESRF ID30B
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 1.41 42.29 99.3 0.037 0.999 17.4 4.3 23909
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 1.41 1.43 99.6 0.656 0.718 2.1 4.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE in house structure 1.41 15.696 23731 1204 99.226 0.181 0.18 0.1883 0.1959 0.2117 28.07
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] -0.824 0.177 0.647
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.036 r_dihedral_angle_4_deg 16.238 r_dihedral_angle_3_deg 11.743 r_lrange_it 5.622 r_lrange_other 5.579 r_dihedral_angle_1_deg 4.625 r_scangle_it 3.807 r_scangle_other 3.805 r_mcangle_it 2.579 r_mcangle_other 2.577
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.036 r_dihedral_angle_4_deg 16.238 r_dihedral_angle_3_deg 11.743 r_lrange_it 5.622 r_lrange_other 5.579 r_dihedral_angle_1_deg 4.625 r_scangle_it 3.807 r_scangle_other 3.805 r_mcangle_it 2.579 r_mcangle_other 2.577 r_scbond_it 2.305 r_scbond_other 2.303 r_mcbond_it 1.578 r_mcbond_other 1.564 r_angle_other_deg 1.254 r_angle_refined_deg 1.128 r_nbd_refined 0.195 r_nbtor_refined 0.171 r_symmetry_nbd_other 0.165 r_symmetry_nbd_refined 0.152 r_nbd_other 0.137 r_xyhbond_nbd_refined 0.109 r_symmetry_xyhbond_nbd_refined 0.103 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.063 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 921 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling