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Crystal Structure of the bromodomain of human transcription activator BRG1 (SMARCA4) in complex with 2-(6-amino-5-(piperazin-1-yl)pyridazin-3-yl)phenol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DKD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Crystallization buffer: 20% medium-molecular-weight PEG smear, 0.1 M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.25 45.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.18 α = 90 b = 64.91 β = 100.88 c = 48.77 γ = 90
Symmetry Space Group P 1 21 1
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 2M 2017-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91842 BESSY 14.2
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 1.57 47.3 99.8 0.061 0.998 16.1 6.2 35278 12.1272343356
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 1.57 1.6 99.7 0.246 0.973 6.8
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 5DKD 1.57 34.2487331998 1.36039202951 35224 1741 99.7112608277 0.180774575223 0.178958143499 0.1803 0.215317979354 0.2132 16.3242338323
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 15.6696321893 f_angle_d 0.772781691468 f_chiral_restr 0.0457401167629 f_bond_d 0.00532032902259 f_plane_restr 0.00404596235641
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1951 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing