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N-TERMINAL BROMODOMAIN OF HUMAN BRD4 (3R,4R)-N-cyclohexyl-4-((3-methyl-2-oxo-1,2-dihydro-1,7-naphthyridin-8-yl)amino)piperidine-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 0.1M Hepes pH 7.0, 5% MgCl2, 20% PEG6K
Crystal Properties Matthews coefficient Solvent content 2.16 42.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.43 α = 90 b = 48.98 β = 90 c = 61.24 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 PILATUS3 6M 2013-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9200 Diamond I04-1
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 1.26 16.66 99.1 0.043 0.999 27.4 6.2 35636
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 1.26 1.29 95.5 0.551 0.818 2.5
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 MOLECULAR REPLACEMENT FREE R-VALUE in house structure 1.26 16.657 35566 1782 98.858 0.197 0.1957 0.2037 0.2138 0.2191 19.953
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] 0.482 0.325 -0.807
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.481 r_dihedral_angle_3_deg 11.934 r_dihedral_angle_4_deg 9.661 r_lrange_it 5.513 r_dihedral_angle_1_deg 4.919 r_lrange_other 4.886 r_scangle_it 2.353 r_scangle_other 2.351 r_mcangle_it 1.923 r_mcangle_other 1.921
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.481 r_dihedral_angle_3_deg 11.934 r_dihedral_angle_4_deg 9.661 r_lrange_it 5.513 r_dihedral_angle_1_deg 4.919 r_lrange_other 4.886 r_scangle_it 2.353 r_scangle_other 2.351 r_mcangle_it 1.923 r_mcangle_other 1.921 r_scbond_other 1.395 r_scbond_it 1.394 r_angle_other_deg 1.176 r_angle_refined_deg 1.159 r_mcbond_it 1.132 r_mcbond_other 1.132 r_nbd_refined 0.185 r_symmetry_nbd_refined 0.182 r_nbtor_refined 0.169 r_nbd_other 0.168 r_symmetry_nbd_other 0.162 r_xyhbond_nbd_refined 0.109 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_refined 0.064 r_chiral_restr 0.055 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 258 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling