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Crystal Structure of BRD4(D1) with 4-[4-(4-bromophenyl)-1-(piperidin-4-yl)-1H-imidazol-5-yl]-N-(3,5-dimethylphenyl)pyrimidin-2-amine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JT4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.31 46.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.106 α = 90 b = 59.345 β = 90 c = 111.443 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 EIGER X 16M 2019-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9791 APS 24-ID-E
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 1.41 111.44 99.7 0.049 0.999 16 5.7 54825 20.63
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 0.726 0.655
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7jt4 1.41 55.72 1.38 54744 2644 99.6 0.1517 0.1499 0.152 0.1858 0.1864 27.3
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.7857 f_angle_d 1.2186 f_chiral_restr 0.1018 f_bond_d 0.0134 f_plane_restr 0.0096
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2099 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 82
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing