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C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1-benzyl-N-methyl-2-oxo-1,2-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 6.5 293 30% PEG 300, 0.1M MES buffer pH6.5
Crystal Properties Matthews coefficient Solvent content 2.29 46.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.106 α = 90 b = 52.758 β = 90 c = 32.318 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 2014-08-07 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 1.61 36.05 95.5 0.019 31.9 2.7 15692
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 1.61 1.7 81.8 0.065 11.2 1.8
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 1.613 29.491 15647 787 94.721 0.141 0.1393 0.1429 0.1775 0.181 14.632
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] 0.012 0.017 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.653 r_dihedral_angle_4_deg 23.709 r_dihedral_angle_3_deg 12.475 r_lrange_it 5.912 r_lrange_other 5.91 r_dihedral_angle_1_deg 5.334 r_scangle_it 2.206 r_scangle_other 2.204 r_mcangle_other 1.509 r_mcangle_it 1.506
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.653 r_dihedral_angle_4_deg 23.709 r_dihedral_angle_3_deg 12.475 r_lrange_it 5.912 r_lrange_other 5.91 r_dihedral_angle_1_deg 5.334 r_scangle_it 2.206 r_scangle_other 2.204 r_mcangle_other 1.509 r_mcangle_it 1.506 r_angle_other_deg 1.409 r_scbond_other 1.345 r_scbond_it 1.343 r_angle_refined_deg 1.325 r_mcbond_it 0.906 r_mcbond_other 0.835 r_nbd_refined 0.214 r_nbtor_refined 0.178 r_symmetry_nbd_other 0.174 r_nbd_other 0.139 r_symmetry_nbd_refined 0.124 r_xyhbond_nbd_refined 0.118 r_symmetry_xyhbond_nbd_refined 0.114 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.079 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 941 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling